A computational model of familiarity detection for natural pictures, abstract images, and random patterns: Combination of deep learning and anti-Hebbian training.

We present a neural network model for familiarity recognition of different types of images in the perirhinal cortex (the FaRe model). The model is designed as a two-stage system. At the first stage, the parameters of an image are extracted by a pretrained deep learning convolutional neural network.

Differentiating ictal/subclinical spikes and waves in childhood absence epilepsy by spectral and network analyses: A pilot study.

Objective: Childhood absence epilepsy (CAE) is a disease with distinct seizure semiology and electroencephalographic (EEG) features. Differentiating ictal and subclinical generalized spikes and waves discharges (GSWDs) in the EEG is challenging, since they appear to be identical upon visual inspection. Here, spectral and functional connectivity (FC) analyses were applied to routine EEG data of CAE patients, to differentiate ictal and subclinical GSWDs.

[Antibacterial effects of peptides synthesized based on the sequence of ribosome protein S1].

Antibiotic resistance of bacteria is a topical problem on a global scale. Sometimes vigorous human activity leads to an increase in the number of bacteria carrying resistance genes in the environment. Antimicrobial peptides (AMPs) and similar compounds are potential candidates for combating antibiotic-resistant bacteria.

The Classification of Short Scientific Texts Using Pretrained BERT Model.

Automated text classification is a natural language processing (NLP) technology that could significantly facilitate scientific literature selection. A specific topical dataset of 630 article abstracts was obtained from the PubMed database. We proposed 27 parametrized options of PubMedBERT model and 4 ensemble models to solve a binary classification task on that dataset.

Global data on earthworm abundance, biomass, diversity and corresponding environmental properties.

Earthworms are an important soil taxon as ecosystem engineers, providing a variety of crucial ecosystem functions and services. Little is known about their diversity and distribution at large spatial scales, despite the availability of considerable amounts of local-scale data. Earthworm diversity data, obtained from the primary literature or provided directly by authors, were collated with information on site locations, including coordinates, habitat cover, and soil properties.

IKI GRB-FuN: observations of GRBs with small-aperture telescopes.

Gamma-ray bursts (GRBs) are the most energetic and mysterious events in the Universe, which are observed in all ranges of electromagnetic spectrum. Most valuable results about physics of GRB are obtained by optical observations. GRBs are initially detected in gamma-rays with poor localization accuracy, and an optical counterpart should be found.

Landscape of allele-specific transcription factor binding in the human genome.

Sequence variants in gene regulatory regions alter gene expression and contribute to phenotypes of individual cells and the whole organism, including disease susceptibility and progression. Single-nucleotide variants in enhancers or promoters may affect gene transcription by altering transcription factor binding sites. Differential transcription factor binding in heterozygous genomic loci provides a natural source of information on such regulatory variants.

On the suitability of using the diagonal Gaussian approximation in the calculation of the magnitude-based likelihood function.

Statistical likelihood maximization is currently one of the main tools in computational procedures in biological crystallography. In these procedures, the likelihood function is calculated, as a rule, within the framework of a diagonal Gaussian approximation (DGA) of the joint probability distribution of the real and imaginary parts of a set of structure factors. This approximation assumes pairwise uncorrelated values of various structure-factor components.

Persistent fluctuations of the swarm size of Brownian bees.

The "Brownian bees" model describes a system of N-independent branching Brownian particles. At each branching event the particle farthest from the origin is removed so that the number of particles remains constant at all times. Berestycki et al.

Hybrid Polycarbosilane-Siloxane Dendrimers: Synthesis and Properties.

A series of carbosilane dendrimers of the 4th, 6th, and 7th generations with a terminal trimethylsilylsiloxane layer was synthesized. Theoretical models of these dendrimers were developed, and equilibrium dendrimer conformations obtained via molecular dynamics simulations were in a good agreement with experimental small-angle X-ray scattering (SAXS) data demonstrating molecule monodispersity and an almost spherical shape. It was confirmed that the glass transition temperature is independent of the dendrimer generation, but is greatly affected by the chemical nature of the dendrimer terminal groups.

Adsorption of Silicon-Containing Dendrimers: Effects of Chemical Composition, Structure, and Generation Number.

We studied the conformational behavior of silicon-containing dendrimers during their adsorption onto a flat impenetrable surface by molecular dynamics (MD) simulations. Four homologous series of dendrimers from the 4th up to the 7th generations were modeled, namely, two types of carbosilane dendrimers differing by the functionality of the core Si atom and two types of siloxane dendrimers with different lengths of the spacers. Comparative analysis of the fractions of adsorbed atoms belonging to various structural layers within dendrimers as well as density profiles allowed us to elucidate not only some general trends but also the effects determined by dendrimer specificity.

Search and study of the space debris and asteroids within ISON project.

International Scientific Optical Network (ISON) is an open international voluntary project specializing in observations of the near-Earth space objects. Observatories collaborating with ISON provide the global coverage and successfully combine the observations of the space debris and asteroids. The network includes more than 50 telescopes of 27 observatories in 15 countries and has been working since 2005.

A simple method defines 3D morphology and axon projections of filled neurons in a small CNS volume: Steps toward understanding functional network circuitry.

Background: Fundamental to understanding neuronal network function is defining neuron morphology, location, properties, and synaptic connectivity in the nervous system. A significant challenge is to reconstruct individual neuron morphology and connections at a whole CNS scale and bring together functional and anatomical data to understand the whole network.

New Method: We used a PC controlled micropositioner to hold a fixed whole mount of Xenopus tadpole CNS and replace the stage on a standard microscope.

Bioinformatics Analysis of Actin Molecules: Why Quantity Does Not Translate Into Quality?

It is time to review all the available data and find the distinctive characteristics of actin that make it such an important cell molecule. The presented double-stranded organization of filamentous actin cannot explain the strong polymorphism of actin fibrils. In this work, we performed bioinformatics analysis of a set of 296 amino acid actin sequences from representatives of different classes of the Chordate type.

Is there any intron sliding in mammals?

Background: Eukaryotic protein-coding genes consist of exons and introns. Exon-intron borders are conserved between species and thus their changes might be observed only on quite long evolutionary distances. One of the rarest types of change, in which intron relocates over a short distance, is called "intron sliding", but the reality of this event has been debated for a long time.

Communities of ground beetles (Carabidae, Coleoptera) in broad-leaved forests of protected and urban areas of the Kaluga Oblast (European Russia).

Background: This sampling-event dataset provides primary data about species diversity, population and seasonal activity of ground beetles (Carabidae, Coleoptera). The study was carried out in broad-leaved forests of protected ("Kaluzhskiye Zaseki" Nature Reserve and Ugra National Park) and urban areas (the Kaluga City) of the Kaluga Oblast. Carabids were collected from April to October during 1995-1998 by pitfall traps.

Diversity of Collembola under various types of anthropogenic load on ecosystems of European part of Russia.

Background: Despite the key role played by soil organisms in the functioning of terrestrial ecosystems and provisioning of ecosystem services (Barrios 2007, Bardgett and Putten 2014), available open data on soil biodiversity are incongruously scarce (Eisenhauer 2017, Cameron 2018). This is especially true for Russia, but contrasts long traditions of soil zoological research and large volumes of data that were collected during the second half of the 20 century for the territory of the former USSR. Last year, 41,928 georeferenced occurrences of soil-dwelling arthropods Collembola were digitised and published through GBIF.

New Model for Stacking Monomers in Filamentous Actin from Skeletal Muscles of .

To date, some scientific evidence (limited proteolysis, mass spectrometry analysis, electron microscopy (EM)) has accumulated, which indicates that the generally accepted model of double-stranded of filamentous actin (F-actin) organization in eukaryotic cells is not the only one. This entails an ambiguous understanding of many of the key cellular processes in which F-actin is involved. For a detailed understanding of the mechanism of F-actin assembly and actin interaction with its partners, it is necessary to take into account the polymorphism of the structural organization of F-actin at the molecular level.

Molecular modeling and computational study of the chiral-dependent structures and properties of the self-assembling diphenylalanine peptide nanotubes, containing water molecules.

DFT (VASP) and semi-empirical (HyperChem) calculations for the L- and D-chiral diphenylalanine (L-FF and D-FF) nanotube (PNT) structures, empty and filled with water/ice clusters, are presented and analyzed. The results obtained show that after optimization, the dipole moment and polarization of both chiral type L-FF and D-FF PNT and embedded water/ice cluster are enhanced; the water/ice cluster acquire the helix-like structure similar as L-FF and D-FF PNT. Ferroelectric properties of tubular water/ice helix-like-cluster obtained after optimization inside L-FF and D-FF PNT and total L-FF and D-FF PNT with embedded water/ice cluster are discussed.

Physical Fundamentals of Biomaterials Surface Electrical Functionalization.

This article is focusing on electrical functionalization of biomaterial's surface to enhance its biocompatibility. It is an overview of previously unpublished results from a series of experiments concerning the effects surface electrical functionalization can have on biological systems. cells were used for biological experiments.

Structures and Properties of the Self-Assembling Diphenylalanine Peptide Nanotubes Containing Water Molecules: Modeling and Data Analysis.

The structures and properties of the diphenylalanine (FF) peptide nanotubes (PNTs), both L-chiral and D-chiral (L-FF and D-FF) and empty and filled with water/ice clusters, are presented and analyzed. DFT (VASP) and semi-empirical calculations (HyperChem) to study these structural and physical properties of PNTs (including ferroelectric) were used. The results obtained show that after optimization the dipole moment and polarization of both chiral type L-FF and D-FF PNT and embedded water/ice cluster are enhanced; the water/ice cluster acquire the helix-like structure similar as L-FF and D-FF PNT.

Polarization Switching in 2D Nanoscale Ferroelectrics: Computer Simulation and Experimental Data Analysis.

The polarization switching kinetics of nanosized ferroelectric crystals and the transition between homogeneous and domain switching in nanoscale ferroelectric films are considered. Homogeneous switching according to the Ginzburg-Landau-Devonshire (LGD) theory is possible only in two-dimensional (2D) ferroelectrics. The main condition for the applicability of the LGD theory in such systems is its homogeneity along the polarization switching direction.

Velocity fluctuations of stochastic reaction fronts propagating into an unstable state: Strongly pushed fronts.

The empirical velocity of a reaction-diffusion front, propagating into an unstable state, fluctuates because of the shot noises of the reactions and diffusion. Under certain conditions these fluctuations can be described as a diffusion process in the reference frame moving with the average velocity of the front. Here we address pushed fronts, where the front velocity in the deterministic limit is affected by higher-order reactions and is therefore larger than the linear spread velocity.

Analytic description of anomalous diffusion in heterogeneous environments: Fokker-Planck equation without fractional derivatives.

This article presents a one-dimensional model of diffusion in a heterogeneous environment, which qualitatively reflects the transport properties of a polymeric membrane with carbon nanotube areas. We derive the Fokker-Planck equation from a system of stochastic equations using a diffusion regime in polymers and a ballistic diffusion regime in nanotube areas. We demonstrate how the probability density function changes in the presence of nanotubes.