Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome Memory Limitation.

This work introduces a new faster implementation of the hydrogen bond network (complex arrangement of hydrogen bonds between or within molecules) search algorithm in biomacromolecules and their environment. Existing implementation of such an algorithm in GROMACS [Abraham et al. .

DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in Trajectories.

This work describes a fast implementation of a software algorithm associated with determination of protein secondary structure based on the Define Secondary Structure of Proteins (DSSP) algorithm. This implementation is fully compatible with the DSSP v.4 and DSSP v.

An IoT-Enabled E-Nose for Remote Detection and Monitoring of Airborne Pollution Hazards Using LoRa Network Protocol.

Detection and monitoring of airborne hazards using e-noses has been lifesaving and prevented accidents in real-world scenarios. E-noses generate unique signature patterns for various volatile organic compounds (VOCs) and, by leveraging artificial intelligence, detect the presence of various VOCs, gases, and smokes onsite. Widespread monitoring of airborne hazards across many remote locations is possible by creating a network of gas sensors using Internet connectivity, which consumes significant power.

A Smart Card-Based Two-Factor Mutual Authentication Scheme for Efficient Deployment of an IoT-Based Telecare Medical Information System.

The integration of the Internet of Things (IoT) and the telecare medical information system (TMIS) enables patients to receive timely and convenient healthcare services regardless of their location or time zone. Since the Internet serves as the key hub for connection and data sharing, its open nature presents security and privacy concerns and should be considered when integrating this technology into the current global healthcare system. Cybercriminals target the TMIS because it holds a lot of sensitive patient data, including medical records, personal information, and financial information.

NOMA-Based VLC Systems: A Comprehensive Review.

The enhanced proliferation of connected entities needs a deployment of innovative technologies for the next generation wireless networks. One of the critical concerns, however, is the spectrum scarcity, due to the unprecedented broadcast penetration rate nowadays. Based on this, visible light communication (VLC) has recently emerged as a viable solution to secure high-speed communications.

A Survey of Deep Learning Based NOMA: State of the Art, Key Aspects, Open Challenges and Future Trends.

Non-Orthogonal Multiple Access (NOMA) has become a promising evolution with the emergence of fifth-generation (5G) and Beyond-5G (B5G) rollouts. The potentials of NOMA are to increase the number of users, the system's capacity, massive connectivity, and enhance the spectrum and energy efficiency in future communication scenarios. However, the practical deployment of NOMA is hindered by the inflexibility caused by the offline design paradigm and non-unified signal processing approaches of different NOMA schemes.

Inside and outside of virus-like particles HBc and HBc/4M2e: A comprehensive study of the structure.

Hepatitis B virus core antigen (HBc) with the insertion of four external domains of the influenza A M2 protein (HBc/4M2e) form virus-like particles whose structure was studied using a combination of molecular modeling and cryo-electron microscopy (cryo-EM). It was also shown that self-assembling of the particles occurs inside bacterial cells, but despite the big inner volume of the core shell particle, purified HBc/4M2e contain an insignificant amount of bacterial proteins. It was shown that a fragment of the M2e corresponding to 4M2e insertion is prone to formation of amyloid-like fibrils.

Incidence of Common Herpesviruses in Colonic Mucosal Biopsies Following Hematopoietic Stem Cell Transplantation.

Intestinal complications are common after allogeneic hematopoietic stem cell transplantation (allo-HSCT). However, only scarce data concern herpesvirus incidence in the colonic mucosa post-HSCT. Our purpose was to assess the frequency and clinical significance of cytomegalovirus (CMV), Epstein−Barr virus (EBV), human herpesvirus type 6 (HHV6), and herpes simplex virus (HSV) in the colonic mucosa post-HSCT.

Caught red handed: modeling and confirmation of the myeloperoxidase ceruloplasmin alpha-thrombin complex.

The work is devoted to the study of the structural characteristics of the myeloperoxidase-ceruloplasmin-thrombin complex using small-angle neutron scattering methods in combination with computer modeling, as well as surface plasmon resonance and solid-phase enzyme assay. We have previously shown that the functioning of active myeloperoxidase during inflammation, despite the presence in the blood of an excess of ceruloplasmin which inhibits its activity, is possible due to the partial proteolysis of ceruloplasmin by thrombin. In this study, the myeloperoxidase-ceruloplasmin-thrombin heterohexamer was obtained in vitro.

Zero-Padding and Spatial Augmentation-Based Gas Sensor Node Optimization Approach in Resource-Constrained 6G-IoT Paradigm.

Ultra-low-power is a key performance indicator in 6G-IoT ecosystems. Sensor nodes in this eco-system are also capable of running light-weight artificial intelligence (AI) models. In this work, we have achieved high performance in a gas sensor system using Convolutional Neural Network (CNN) with a smaller number of gas sensor elements.

Phylogenetic Characteristics of West Nile Virus Isolated From Mosquitoes in West Kazakhstan.

West Nile virus is widespread in southern Russia, where the fever appears annually. Since Western Kazakhstan borders on southern Russia, we examined mosquitoes in this region for the presence of West Nile virus. Virus was detected in a small proportion of mosquitoes (3/239 pools) and isolates are related to strains from Volgograd, Russia.

[Fecal microbiota transplantation for graft-versus-host disease in children and adults: methods, clinical effects, safety].

Aim: Was to evaluate clinical efficacy, adverse events and changes in the gut microbiome after fecal microbiota transplantation (FMT) in patients with gastrointestinal (GI) form of graft-versus-host disease (GVHD).

Materials And Methods: The prospective single-center study in R.M.

Cold and distant: structural features of the nucleoprotein complex of a cold-adapted influenza A virus strain.

Two influenza A nucleoprotein variants (wild-type: G102R; and mutant: G102R and E292G) were studied with regard to macro-molecular interactions in oligomeric form (24-mers). The E292G mutation has been previously shown to provide cold adaptation. Molecular dynamics simulations of these complexes and trajectory analysis showed that the most significant difference between the obtained models was distance between nucleoprotein complex strands.

Thermostability improvement of Aspergillus awamori glucoamylase via directed evolution of its gene located on episomal expression vector in Pichia pastoris cells.

Novel thermostable variants of glucoamylase (GA) from filamentous fungus Aspergillus awamori X100 were constructed using the directed evolution approach based on random mutagenesis by error-prone PCR of the catalytic domain region of glucoamylase gene located on a new episomal expression vector pPEHα in Pichia pastoris cells. Out of 3000 yeast transformants screened, six new thermostable GA variants with amino acid substitutions Val301Asp, Thr390Ala, Thr390Ala/Ser436Pro, Leu7Met/His391Tyr, Asn9His/Ile82Phe and Ser8Arg/Gln338Leu were identified and studied. To estimate the effect of each substitution in the double mutants, we have constructed the relevant single mutants of GA by site-directed mutagenesis and analyzed their thermal properties.

SAW RFID Devices Using Connected IDTs as an Alternative to Conventional Reflectors for Harsh Environments.

Remote interrogation of surface acoustic wave identification tag (ID-tags) imposes a high signal amplitude which is related to a high coupling coefficient value ( K ) and low propagation losses ( α ). In this article, we propose and discuss an alternative configuration to the standard one. Here, we replaced the conventional configuration, i.

Effects of surface halogenation on exciton relaxation in Si crystallites: prospects for photovoltaics.

Ab initio study of Si crystallites (diameter: 1.1-2.4 nm) with fully Cl- or Br-passivated surfaces was performed.

Peroral Endoscopic Myotomy in Diffuse Thickened Esophageal Wall in an Adolescent.

Achalasia is an extremely rare pathology in children. Peroral endoscopic myotomy (POEM) is the gold standard for the surgical treatment of achalasia in adults, but only a limited number of cases of achalasia treatment using POEM in children have been published in the literature. Sometimes, high-resolution manometry signs of achalasia can mimic diffuse esophageal leiomyoma.

A double-edged sword: supramolecular complexes of triazavirine display multicenter binding effects which influence aggregate formation.

Communicated by Ramaswamy H. Sarma.

High-Temperature SAW Resonator Sensors: Electrode Design Specifics.

Surface acoustic wave (SAW) sensors are steadily paving the way to wider application areas. Their main benefit consisting in the possibility of wireless interrogation with the radio frequency interrogation signal being the only energy source for the reradiated signal. This feature is getting more and more attractive with the growing demand in monitoring multiple industrial objects difficult to access by wired sensors in harsh environments.

The amyloidogenicity of the influenza virus PB1-derived peptide sheds light on its antiviral activity.

The influenza virus polymerase complex is a promising target for new antiviral drug development. It is known that, within the influenza virus polymerase complex, the PB1 subunit region from the 1st to the 25th amino acid residues has to be is in an alpha-helical conformation for proper interaction with the PA subunit. We have previously shown that PB1(6-13) peptide at low concentrations is able to interact with the PB1 subunit N-terminal region in a peptide model which shows aggregate formation and antiviral activity in cell cultures.

Triazavirine supramolecular complexes as modifiers of the peptide oligomeric structure.

In this study, we present molecular dynamics simulations of the antiviral drug triazavirine, that affects formation of amyloid-like fibrils of the model peptide (SI). According to our simulations, triazavirine is able to form linear supramolecular structures which can act as shields and prevent interactions between SI monomers. This model, as validated by simulations, provides an adequate explanation of triazavirine's mechanism of action as it pertains to SI peptide fibril formation.

Characterization of the cleaved edge cross section of the heterostructures with GaMnAs layer by the confocal micro-Raman spectroscopy.

Confocal micro-Raman spectroscopy was used to measure cross-section linescans of the cleaved edge of heterostructures involving a GaMnAs layer. The investigations revealed a shift of the TO mode in the compressed GaMnAs layer to high frequencies relative to the TO GaAs mode in the substrate and to low frequencies in the tensile GaMnAs layers. These results are in agreement with the different manifestations of the anomalous Hall effect in the GaMnAs layers, with either compressive or tensile strains.

Effects of Experimental Coma on the Expression of Bcl-2 Protein and Caspases 3 and 9 in Rat Brain.

We performed immunohistochemical analysis of the expression of caspases 3, 9 and bcl-2 protein in rat brain at various terms after administration of LD50 of sodium thiopental. Expression of the specified apoptosis markers was found in the sensorimotor cortex and hippocampus (dentate gyrus and CA2 region).