Negative linear compressibility of molecular and ionic-molecular crystals.

The compressibility of crystalline tetrabromophthalic anhydride (TBPA) and 1-ethyl-3-methylimidazolium nitrate (EMN) was studied based on density functional theory including dispersion interactions at pressures below 1 GPa. It is found for the first time that EMN demonstrates negative linear compressibility (NLC) up to ∼0.15 GPa, whereas TBPA shows significant NLC at pressures higher than ∼0.

Increased Levels of hsa-miR-199a-3p and hsa-miR-382-5p in Maternal and Neonatal Blood Plasma in the Case of Placenta Accreta Spectrum.

Despite the increasing number of placenta accreta spectrum (PAS) cases in recent years, its impact on neonatal outcomes and respiratory morbidity, as well as the underlying pathogenetic mechanism, has not yet been extensively studied. Moreover, no study has yet demonstrated the effectiveness of antenatal corticosteroid therapy (CT) for the prevention of respiratory distress syndrome (RDS) in newborns of mothers with PAS at the molecular level. In this regard, microRNA (miRNA) profiling by small RNA deep sequencing and quantitative real-time PCR was performed on 160 blood plasma samples from preterm infants (gestational age: 33-36 weeks) and their mothers who had been diagnosed with or without PAS depending on the timing of the antenatal RDS prophylaxis.

Effect of Drug-to-Protein Reaction Kinetics on the Results of Thermal Proteome Profiling.

In this Letter, a two-term formalism for constructing protein solubility curves in thermal proteome profiling (TPP) is considered, which takes into account the efficiency of the drug-protein binding reaction. When the reaction is incomplete, this results in distortion of the otherwise sigmoidal shape of the curve after drug treatment, which is often observed in experiments. This distortion may be significant enough to disqualify the corresponding protein from the list of drug target candidates, thus negatively affecting the results of TPP data analysis.

First-principles molecular dynamics of exciton-driven initial stage of plasma phase transition in warm dense molecular nitrogen.

Understanding the properties of molecular nitrogen N2 at extreme conditions is the fundamental problem for atomistic theory and the important benchmark for the capabilities of first-principles molecular dynamics (FPMD) methods. In this work, we focus on the connection between the dynamics of ions and electronic excitations in warm dense N2. The restricted open-shell Kohn-Sham method gives us the possibility to reach relevant time and length scales for FPMD modeling of an isolated exciton dynamics in warm dense N2.

Ultrafast Proteomics.

Current stage of proteomic research in the field of biology, medicine, development of new drugs, population screening, or personalized approaches to therapy dictates the need to analyze large sets of samples within the reasonable experimental time. Until recently, mass spectrometry measurements in proteomics were characterized as unique in identifying and quantifying cellular protein composition, but low throughput, requiring many hours to analyze a single sample. This was in conflict with the dynamics of changes in biological systems at the whole cellular proteome level upon the influence of external and internal factors.

On the utility of ultrafast MS1-only proteomics in drug target discovery studies based on thermal proteome profiling method.

Advances in high-throughput high-resolution mass spectrometry and the development of thermal proteome profiling approach (TPP) have made it possible to accelerate a drug target search. Since its introduction in 2014, TPP quickly became a method of choice in chemical proteomics for identifying drug-to-protein interactions on a proteome-wide scale and mapping the pathways of these interactions, thus further elucidating the unknown mechanisms of action of a drug under study. However, the current TPP implementations based on tandem mass spectrometry (MS/MS), associated with employing lengthy peptide separation protocols and expensive labeling techniques for sample multiplexing, limit the scaling of this approach for the ever growing variety of drug-to-proteomes.

Diagnostic Role of Cell-Free miRNAs in Identifying Placenta Accreta Spectrum during First-Trimester Screening.

Placenta accreta spectrum (PAS) is a severe complication of pregnancy associated with excessive invasion of cytotrophoblast cells at the sites of the endometrial-myometrial interface and the myometrium itself in cases of adherent (creta) and invasive (increta and percreta) forms, respectively. This leads to a high risk of massive blood loss, maternal hysterectomy, and preterm birth. Despite advancements in ultrasound protocols and found associations of alpha-fetoprotein, PAPP-A, hCG, PLGF, sFlt-1, IL-8, and IL-33 peripheral blood levels with PAS, there is a high need for an additional non-invasive test to improve the diagnostic accuracy and to select the real PAS from the suspected ones in the first-trimester screening.

Extracellular vesicles of human glial cells exert neuroprotective effects via brain miRNA modulation in a rat model of traumatic brain injury.

Stem cell-based therapeutic approaches for neurological disorders are widely studied. Paracrine factors secreted by stem cells in vitro and delivered intranasally might allow bypassing the disadvantages associated with a surgical cell delivery procedure with likely immune rejection of a transplant. In this study, we investigated the therapeutic effect of the extracellular vesicles secreted by glial progenitor cells (GPC-EV) derived from human induced pluripotent stem cell in a traumatic brain injury model.

Blood Plasma Small Non-Coding RNAs as Diagnostic Molecules for the Progesterone-Receptor-Negative Phenotype of Serous Ovarian Tumors.

The expression level of the progesterone receptor (PGR) plays a crucial role in determining the biological characteristics of serous ovarian carcinoma. Low PGR expression is associated with chemoresistance and a poorer outcome. In this study, our objective was to explore the relationship between tumor progesterone receptor levels and RNA profiles (miRNAs, piwiRNAs, and mRNAs) to understand their biological characteristics and behavior.

Prediction of Early- and Late-Onset Pre-Eclampsia in the Preclinical Stage via Placenta-Specific Extracellular miRNA Profiling.

Pre-eclampsia (PE) is one of the severe complications of pregnancy in 3-8% of all cases and is one of the leading causes of maternal and perinatal mortality. The fundamental role in the pathogenesis of PE is assigned to maternal and/or placental factors, whereby the combination and manifestation of which determines the time of onset of the clinical symptoms of PE (before or after 34 weeks of gestation) and their severity. It is known that the expression level of miRNAs, the regulators of signaling cascades in the cell, depends on gestational age.

Search for New Participants in the Pathogenesis of High-Grade Serous Ovarian Cancer with the Potential to Be Used as Diagnostic Molecules.

Recent studies have attempted to develop molecular signatures of epithelial ovarian cancer (EOC) based on the quantitation of protein-coding and non-coding RNAs to predict disease prognosis. Due to the heterogeneity of EOC, none of the developed prognostic signatures were directly applied in clinical practice. Our work focuses on high-grade serous ovarian carcinoma (HGSOC) due to the highest mortality rate relative to other types of EOC.

Host nucleases generate prespacers for primed adaptation in the type I-E CRISPR-Cas system.

CRISPR-Cas systems provide prokaryotes with adaptive immunity against foreign nucleic acids. In , immunity is acquired upon integration of 33-bp spacers into CRISPR arrays. DNA targets complementary to spacers get degraded and serve as a source of new spacers during a process called primed adaptation.

Exciton Nature of Plasma Phase Transition in Warm Dense Fluid Hydrogen: ROKS Simulation.

The transition of warm dense fluid hydrogen from an insulator to a conducting state at pressures of about 20-400 GPa and temperatures of 500-5000 K has been the subject of active scientific research over the past few decades. However, various experimental and theoretical methods do not provide consistent results. In this work, we have applied the restricted open-shell Kohn-Sham (ROKS) method for first principles molecular dynamics of dense hydrogen after thermal excitation to the first singlet excited state.

Mass Spectrometry-Based Chemical Proteomics for Drug Target Discoveries.

Chemical proteomics, emerging rapidly in recent years, has become a main approach to identifying interactions between the small molecules and proteins in the cells on a proteome scale and mapping the signaling and/or metabolic pathways activated and regulated by these interactions. The methods of chemical proteomics allow not only identifying proteins targeted by drugs, characterizing their toxicity and discovering possible off-target proteins, but also elucidation of the fundamental mechanisms of cell functioning under conditions of drug exposure or due to the changes in physiological state of the organism itself. Solving these problems is essential for both basic research in biology and clinical practice, including approaches to early diagnosis of various forms of serious diseases or prediction of the effectiveness of therapeutic treatment.

Research into Morphofunctional Characteristics of Erythrocytes in COVID-19 Patients.

In this paper, the erythrocytes of healthy donors and people with a confirmed diagnosis of COVID-19 were tested by Raman spectroscopy and laser interference microscopy. We argue that erythrocytes (red blood cells) in COVID-19 patients have an irregular shape, and their morphometric characteristics are impaired in comparison to healthy red blood cells. Raman spectroscopy also allows us to detect a decreased oxygen transport function of these erythrocytes.

Study elastic properties of the leucine and isoleuicine from first principles calculations.

I studied the elastic properties of crystalline L- and DL-forms of leucine and isoleucine within the framework of density functional theory with van der Waals interactions. The energy gaps of the considered crystals are 7.48-7.

A Temporal Boosted YOLO-Based Model for Birds Detection around Wind Farms.

Object detection for sky surveillance is a challenging problem due to having small objects in a large volume and a constantly changing background which requires high resolution frames. For example, detecting flying birds in wind farms to prevent their collision with the wind turbines. This paper proposes a YOLOv4-based ensemble model for bird detection in grayscale videos captured around wind turbines in wind farms.

miRNAs and Their Gene Targets-A Clue to Differentiate Pregnancies with Small for Gestational Age Newborns, Intrauterine Growth Restriction, and Preeclampsia.

Despite the differences in the clinical manifestations of major obstetric syndromes, such as preeclampsia (PE) and intrauterine growth restriction (IUGR), their pathogenesis is based on the dysregulation of proliferation, differentiation, and invasion of cytotrophoblast cells that occur in the developing placenta, decidual endometrium, and myometrial parts of the spiral arteries. To understand the similarities and differences in the molecular mechanisms of PE and IUGR, samples of the placental bed and placental tissue were analyzed using protein mass spectrometry and the deep sequencing of small RNAs, followed by validation of the data obtained by quantitative RT-PCR in real time. A comparison of the transcriptome and proteomic profiles in the samples made it possible to conclude that the main changes in the molecular profile in IUGR occur in the placental bed, in contrast to PE, in which the majority of molecular changes occurs in the placenta.

Clusterin and Its Potential Regulatory microRNAs as a Part of Secretome for the Diagnosis of Abnormally Invasive Placenta: Accreta, Increta, and Percreta Cases.

Magnetic resonance imaging (MRI) and ultrasound methods used for the diagnosis of an abnormally invasive placenta (AIP) have a wide range of sensitivity (Se, 33-93%) and specificity (Sp, 71-100%) levels, which results in a high risk of unfavorable maternal and perinatal outcomes. The relevance of optimizing the diagnosis of AIP is beyond doubt. Given the epigenetic nature of trophoblast invasion, we aimed to quantitate microRNAs and proteins of their target genes that are potentially associated with AIP in blood plasma samples from 64 pregnant women at gestation weeks 30-34 by reverse transcription coupled with polymerase chain reaction (RT-PCR) and Western blotting, respectively.

Study of the Elastic Properties of the Energetic Molecular Crystals Using Density Functionals with van der Waals Corrections.

We studied the elastic properties of crystalline energetic materials within the framework of density functional theory with van der Waals interactions (DFT-D3(BJ) and rev-vdW-DF2). The full sets of elastic constants were computed. The computed parameters are in good agreement with the experimental data.

Small Noncoding RNA Signatures for Determining the Developmental Potential of an Embryo at the Morula Stage.

As part of the optimization of assisted reproductive technology programs, the aim of the study was to identify key small noncoding RNA (sncRNA) molecules that participate in maternal-to-zygotic transition and determine development potential and competence to form a healthy fetus. Small RNA deep sequencing followed by quantitative real-time RT-PCR was used to profile sncRNAs in 50 samples of spent culture medium from morula with different development potentials (no potential (degradation/developmental arrest), low potential (poor-quality blastocyst), and high potential (good/excellent quality blastocyst capable of implanting and leading to live birth)) obtained from 27 subfertile couples who underwent in vitro fertilization. We have shown that the quality of embryos at the morula stage is determined by secretion/uptake rates of certain sets of piRNAs and miRNAs, namely hsa_piR_011291, hsa_piR_019122, hsa_piR_001311, hsa_piR_015026, hsa_piR_015462, hsa_piR_016735, hsa_piR_019675, hsa_piR_020381, hsa_piR_020485, hsa_piR_004880, hsa_piR_000807, hsa-let-7b-5p, and hsa-let-7i-5p.

SSGD: SPARSITY-PROMOTING STOCHASTIC GRADIENT DESCENT ALGORITHM FOR UNBIASED DNN PRUNING.

While deep neural networks (DNNs) have achieved state-of-the-art results in many fields, they are typically over-parameterized. Parameter redundancy, in turn, leads to inefficiency. Sparse signal recovery (SSR) techniques, on the other hand, find compact solutions to overcomplete linear problems.

Combustion of sewage sludge in a fluidized bed of catalyst: ASPEN PLUS model.

This paper presents the results of the simulation of a sewage sludge combustion plant with a productivity of 6 tons per hour using the ASPEN Plus. It is shown that catalytic combustion technology can be used for the efficient utilization of mechanically dehydrated sludge with the moisture of ~75% in autothermal mode (without the use of additional fuel). At the same time, the plant for utilization of 6.

Reproducible Antigen Recognition by the Type I-F CRISPR-Cas System.

CRISPR-associated proteins 1 and 2 (Cas1-2) are necessary and sufficient for new spacer acquisition in some CRISPR-Cas systems (e.g., type I-E), but adaptation in other systems (e.