Analyzing aptamer structure and interactions: in silico modelling and instrumental methods.

Aptamers are short oligonucleotides that bind specifically to various ligands and are characterized by their low immunogenicity, thermostability, and ease of labeling. Many biomedical applications of aptamers as biosensors and drug delivery agents are currently being actively researched. Selective affinity selection with exponential ligand enrichment (SELEX) allows to discover aptamers for a specific target, but it only provides information about the sequence of aptamers; hence other approaches are used for determining aptamer structure, aptamer-ligand interactions and the mechanism of action.

Morpho-physiological digestive features of genetically closely related sympatric lacustrine whitefish forms with different feeding habits.

The effect of different feeding habits on gut morphology and digestive function has been intensively studied during the last decades but sympatric closely related fishes are relatively rare objects of such studies. In the present study, we have identified both morphological and physiological changes in the digestive system of a sympatric pair of whitefish represented by "normal" Coregonus lavaretus pidschian (benthivorous) and "dwarf" C. l.

β-Diketonate Coordination: Vibrational Properties, Electronic Structure, Molecular Topology, and Intramolecular Interactions. Beryllium(II), Copper(II), and Lead(II) as Study Cases.

Nine metal complexes formed by three symmetric β-diketonates (, acetylacetonate (), 1,1,1,3,3,3-hexafluoro-acetylacetonate (), and 2,2,6,6-tetramethylheptane-3,5-dionate ()) and three metal ions (with three different coordination geometries, , Be - tetrahedral, Cu - square planar, and Pb - "swing" square pyramidal) were investigated. The study combines structural analyses, vibrational spectroscopic techniques, and quantum chemical calculations with the aim of bridging crystal structure, electronic structure, molecular topology, and far-infrared (FIR) spectroscopic characteristics. The effect of intramolecular interactions on the structural, electronic, and spectroscopic features is the center of this study.

Infrared photoresponse of GeSiSn p-i-n photodiodes based on quantum dots, quantum wells, pseudomorphic and relaxed layers.

Structural and photoelectric properties of p-i-n photodiodes based on GeSiSn/Si multiple quantum dots both on Si and silicon-on-insulator (SOI) substrates were investigated. Elastic strained state of grown films was demonstrated by x-ray diffractometry. Annealing of p-i-n structures before the mesa fabrication can improve the ideality factor of current-voltage characteristics.

GENA-LM: a family of open-source foundational DNA language models for long sequences.

Recent advancements in genomics, propelled by artificial intelligence, have unlocked unprecedented capabilities in interpreting genomic sequences, mitigating the need for exhaustive experimental analysis of complex, intertwined molecular processes inherent in DNA function. A significant challenge, however, resides in accurately decoding genomic sequences, which inherently involves comprehending rich contextual information dispersed across thousands of nucleotides. To address this need, we introduce GENA language model (GENA-LM), a suite of transformer-based foundational DNA language models capable of handling input lengths up to 36 000 base pairs.

Safety and Efficacy of Tranexamic Acid in General Surgery.

Importance: Perioperative bleeding is common in general surgery. The POISE-3 (Perioperative Ischemic Evaluation-3) trial demonstrated efficacy of prophylactic tranexamic acid (TXA) compared with placebo in preventing major bleeding without increasing vascular outcomes in noncardiac surgery.

Objective: To determine the safety and efficacy of prophylactic TXA, specifically in general surgery.

A comprehensive dataset and neural network approach for named entity recognition in the Uzbek language.

In this study, the authors presented a dataset for named entity recognition in the Uzbek language. The dataset consists of 2000 sentences and 25,865 words, and the sources were legal documents and hand-crafted sentences annotated using the BIOES scheme. The study is complemented by the fact that the authors demonstrated the applications of the created dataset by training a language model using the CNN + LSTM architecture, which achieves high accuracy in NER tasks, with an F1 score of 90.

Double kissing crush versus culotte for bifurcation percutaneous coronary interventions: insights from the PROGRESS-BIFURCATION registry.

Background: Upfront 2-stent techniques are often used in bifurcation percutaneous coronary interventions (PCI), but there is controversy about optimal strategy selection.

Methods: The authors examined the clinical and angiographic characteristics and long-term outcomes of 232 bifurcation PCIs that were performed using the double kissing (DK) crush or culotte technique in 216 patients between 2014 and 2023 using data from the Prospective Global Registry for the Study of Bifurcation Lesion Interventions (NCT05100992). The inverse probability of treatment weighted (IPTW) Cox proportional hazards model was used to assess long-term outcomes.

Infrared photoresponse of GeSiSn p-i-n photodiodes based on quantum dots, quantum wells, pseudomorphic and relaxed layers.

Structural and photoelectric properties of p-i-n photodiodes based on GeSiSn/Si multiple quantum dots both on Si and silicon-on-insulator (SOI) substrates were investigated. Elastic strained state of grown films was demonstrated by x-ray diffractometry. Annealing of p-i-n structures before the mesa fabrication can improve the ideality factor of current-voltage characteristics.

Laser-Induced Olfactory Bulbectomy in Adult Zebrafish as a Novel Putative Model for Affective Syndrome: A Research Tribute to Brian Leonard.

Inducing multiple neurobehavioural and neurochemical deficits, olfactory bulbectomy (OBX) has been developed as a rodent model of depression with potential for antidepressant drug screening. However, the generality of this model in other vertebrate taxa remains poorly understood. A small freshwater teleost fish, the zebrafish (Danio rerio), is rapidly becoming a common model species in neuroscience research.

Epidemiology of Mucopolysaccharidosis Type II According to the Register of the Russian Federation.

Objective: The study aimed to evaluate the epidemiological, clinical, and molecular data of mucopolysaccharidosis type II (MPS II) patients and their outcomes using the national registry of patients in the Russian Federation (RF). Materials and Methods: In the retrospective cohort study, the authors included data from the Russian national registry of MPS II. Results: The prevalence of MPS II in RF is 0.

Deregulation mechanisms and therapeutic opportunities of p53-responsive microRNAs in diffuse large B-cell lymphoma.

Here, we have discussed the molecular mechanisms of p53-responsive microRNAs dysregulation in response to genotoxic stress in diffuse large B-cell lymphoma (DLBCL) patients. The role of micro ribonucleic acids (microRNAs) in p53-signaling cellular stress has been studied. MicroRNAs are the small non-coding RNAs, which regulate genes expression at post-transcriptional level.

Design, synthesis, and evaluation of dehydroabietyl imidazolidine-2,4-diones, 2,4,5-triones, and 2-thioxoimidazolidine-4,5-diones as TDP1 inhibitors and dual TDP1/TDP2 inhibitors.

Tyrosyl DNA phosphodiesterases 1 and 2 (TDP1 and TDP2), which are enzymes involved in the repair of DNA, are regarded as promising targets for the development of new anticancer drugs. In this study, a series of imidazolidine-2,4-diones, 2,4,5-triones, and 2-thioxoimidazolidine-4,5-diones based on dehydroabietylamine (DHAAm) were synthesized. The inhibitory activity of the new compounds against TDP1 and TDP2, as well as their cytotoxic characteristics, were evaluated.

Variability of microbiomes in winter rye, wheat, and triticale affected by snow mold: predicting promising microorganisms for the disease control.

Background: Snow mold caused by different psychrophilic phytopathogenic fungi is a devastating disease of winter cereals. The variability of the snow mold pathocomplex (the quantitative composition of snow mold fungi) has not been evaluated across different crops or different agrocenoses, and no microbial taxa have been predicted at the whole-microbiome level as potential effective snow mold control agents. Our study aimed to assess the variability of the snow mold pathocomplex in different winter cereal crops (rye, wheat, and triticale) in different agrocenoses following the peak disease progression and to arrange a hierarchical list of microbial taxa predicted to be the main candidates to prevent or, conversely, stimulate the development of snow mold pathogens.

Phase transitions, Dirac and Weyl semimetal states in MnGeBiTe.

Using angle-resolved photoemission spectroscopy (ARPES) and density functional theory (DFT), an experimental and theoretical study of changes in the electronic structure (dispersion dependencies) and corresponding modification of the energy band gap at the Dirac point (DP) for topological insulator (TI) [Formula: see text] have been carried out with gradual replacement of magnetic Mn atoms by non-magnetic Ge atoms when concentration of the latter was varied from 10% to 75%. It was shown that when Ge concentration increases, the bulk band gap decreases and reaches zero plateau in the concentration range of 45-60% while trivial surface states (TrSS) are present and exhibit an energy splitting of 100 and 70 meV in different types of measurements. It was also shown that TSS disappear from the measured band dispersions at a Ge concentration of about 40%.

Synthesis and exploration of anticancer potential of spirocyclic 1,2,3-triazoline and aziridine derivatives of natural eudesmanolide isoalantolactone.

Eudesmane-type sesquiterpene lactone isoalantolactone 1 is of great interest due to its availability, biological activity and synthetic application. Respective series of original spirocyclic (11S,5') (1,2,3-triazoline-eudesma-4,15-enolides) and (11S)-aziridine-eudesma-4,15-enolides were efficiently synthesized via a chemoselective 1,3-dipolar cycloaddition reaction of organic azides to the exocyclic double bond of the lactone ring of isoalantolactone or 13E-(aryl)isoalantolactones by heating in DMF or toluene. The thermal reactions of isoalantolactone with benzyl azide, 2-azidoethanol, or n-butyl azide in 2-methoxyethanol afforded 13-(alkyamino)isoalantolactones formed as a mixture of (Z) and (E)-isomers.

The influence of the dry ashing procedure on the correctness of Pb determination in lichens and mosses.

Mosses and lichens are often used to assess atmospheric deposition of Pb. The most widely used method for determining this isotope is gamma spectrometric analysis. There is often a need to enhance the sensitivity of the method, which can be achieved by pre-concentrating Pb.

Hybrid Materials Based on Carbon Nanotubes and Tetra- and Octa-Halogen-Substituted Zinc Phthalocyanines: Sensor Response Toward Ammonia from the Quantum-Chemical Point of View.

This paper presents the results of quantum-chemical modeling performed by the Density Functional-Based Tight Binding (DFTB) method to investigate the change in the band structure of hybrid materials based on carbon nanotubes and unsubstituted, tetra-, or octa-halogen-substituted zinc phthalocyanines upon the adsorption of ammonia molecules. The study showed that the electrical conductivity of these materials and its changes in the case of interaction with ammonia molecules depend on the position of the impurity band formed by the orbitals of macrocycle atoms relative to the forbidden energy gap of the hybrids. The sensor response of the hybrids containing halogenated phthalocyanines was lower by one or two orders of magnitude, depending on the number of substituents, compared to the hybrid with unsubstituted zinc phthalocyanine.

Asymmetry of Motif Conservation Within Their Homotypic Pairs Distinguishes DNA-Binding Domains of Target Transcription Factors in ChIP-Seq Data.

Transcription factors (TFs) are the main regulators of eukaryotic gene expression. The cooperative binding of at least two TFs to genomic DNA is a major mechanism of transcription regulation. Massive analysis of the co-occurrence of overrepresented pairs of motifs for different target TFs studied in ChIP-seq experiments can clarify the mechanisms of TF cooperation.

Position-Dependent Effects of AP Sites Within an Promoter G-Quadruplex Scaffold on Quadruplex Stability and Repair Activity of the APE1 Enzyme.

Apurinic/apyrimidinic (AP) sites are endogenous DNA lesions widespread in human cells. Having no nucleobases, they are noncoding and promutagenic. AP site repair is generally initiated through strand incision by AP endonuclease 1 (APE1).

Synthesis of New Polyfluoro Oligonucleotides via Staudinger Reaction.

Nowadays, nucleic acid derivatives capable of modulating gene expression at the RNA level have gained widespread recognition as promising therapeutic agents. A suitable degree of biological stability of oligonucleotide therapeutics is required for in vivo application; this can be most expeditiously achieved by the chemical modification of the internucleotidic phosphate group, which may also affect their cellular uptake, tissue distribution and pharmacokinetics. Our group has previously developed a strategy for the chemical modification of the phosphate group via the Staudinger reaction on a solid phase of the intermediate dinucleoside phosphite triester and a range of, preferably, electron deficient organic azides such as sulfonyl azides during automated solid-phase DNA synthesis according to the conventional β-cyanoethyl phosphoramidite scheme.

Inhibitory Activity of - and -Functionalized Monoterpene Diols Towards Monoamine Oxidases A and B.

Monoamine oxidase B (MAO-B) inhibitors are widely used as part of combination drug therapy for Parkinson's disease. As demonstrated in both in vitro and in vivo experiments, the monoterpenoid Prottremine and some of its derivatives exhibit high antiparkinsonian activity. In this study, the inhibitory activity of Prottremine and its derivatives (including 14 new 9-- and -derivatives) against MAO-A and MAO-B enzymes has been investigated for the first time.

Changes in the Phenotype and Metabolism of Peritoneal Macrophages in Mucin-2 Knockout Mice and Partial Restoration of Their Functions In Vitro After L-Fucose Treatment.

In the development of inflammatory bowel disease (IBD), peritoneal macrophages contribute to the resident intestinal macrophage pool. Previous studies have demonstrated that oral administration of L-fucose exerts an immunomodulatory effect and repolarizes the peritoneal macrophages in vivo in mice. In this study, we analyzed the phenotype and metabolic profile of the peritoneal macrophages from mice, as well as the effect of L-fucose on the metabolic and morphological characteristics of these macrophages in vitro.

Kinetic Aspects of Ethylene Glycol Degradation Using UV-C Activated Hydrogen Peroxide (HO/UV-C).

Ethylene glycol (EG) is a contaminant in the wastewater of airports because it is commonly used in aircraft deicing fluids during the cold season in northern regions. Ethylene glycol by itself has relatively low toxicity to mammals and aquatic organisms, but it can lead to a substantial increase in chemical and biological oxygen demands. The contamination of water with EG facilitates the rapid growth of microbial biofilms, which decreases the concentration of dissolved oxygen in water and negatively affects overall biodiversity.

High-Resolution NMR of the Hydrogenation Reaction with Parahydrogen in an Inhomogeneous Magnetic Field.

Nuclear magnetic resonance is extremely attractive for operando studies of chemical reactors. However, the heterogeneous catalyst particles placed inside an NMR probe greatly affect the uniformity of the magnetic field. This problem is especially acute when studying heterogeneous hydrogenation processes using parahydrogen.