SNAD: sequence name annotation-based designer

<p>Abstract</p> <p>Background</p> <p>A growing diversity of biological data is tagged with unique identifiers (UIDs) associated with polynucleotides and proteins to ensure efficient computer-mediated data storage, maintenance, and processing. These identifiers, which are not informative for most people, are often substituted by biologically meaningful names in various presentations to facilitate utilization and dissemination of sequence-based knowledge. This substitution is commonly done manually that may be a tedious exercise prone to mistakes and omissions.</p> <p>Results</p> <p>Here we introduce SNAD (Sequence Name Annotation-based Designer) that mediates automatic conversion of sequence UIDs (associated with multiple alignment or phylogenetic tree, or supplied as plain text list) into biologically meaningful names and acronyms. This conversion is directed by precompiled or user-defined templates that exploit wealth of annotation available in cognate entries of external databases. Using examples, we demonstrate how this tool can be used to generate names for practical purposes, particularly in virology.</p> <p>Conclusion</p> <p>A tool for controllable annotation-based conversion of sequence UIDs into biologically meaningful names and acronyms has been developed and placed into service, fostering links between quality of sequence annotation, and efficiency of communication and knowledge dissemination among researchers.</p

Geomagnetic Survey Interpolation with the Machine Learning Approach

This paper portrays the method of UAV magnetometry survey data interpolation. The method accommodates the fact that this kind of data has a spatial distribution of the samples along a series of straight lines (similar to maritime tacks), which is a prominent characteristic of many kinds of UAV surveys. The interpolation relies on the very basic Nearest Neighbours algorithm, although augmented with a Machine Learning approach. Such an approach enables the error of less than 5 percent by intelligently adjusting the Nearest Neighbour algorithm parameters. The method was pilot tested on geomagnetic data with Borok Geomagnetic Observatory UAV aeromagnetic survey data

DEVELOPMENT AND OPTIMIZATION OF AN ULTRA WIDEBAND MINIATURE MEDICAL ANTENNA FOR RADIOMETRIC MULTI-CHANNEL MULTI-FREQUENCY THERMAL MONITORING

The article is devoted to the development of a printed ultra-wideband miniature antenna that can be used for microwave radiometry. An antenna design with a ring-shaped radiator has been proposed, which provides reception of microwave radiation from biological tissues in the 1800–4600 MHz range. The results of mathematical modeling of the antenna electromagnetic field in biological tissues using the finite difference time domain (FDTD) method are presented. Optimization of the antenna design has been carried out to ensure acceptable matching parameters and optimal antenna functionality. The developed antenna has a height of 6 mm and a calculated mass of 5 g; it is planned to manufacture a dielectric substrate based on PDMS polymer with the addition of barium titanate. The issues of calculating the antenna parameters (measurement depth, resolution and distribution of radiation power over the volume of biological tissue, sensitivity, etc.) are considered. The research results and design parameters of the developed antenna demonstrated the effectiveness of the new antenna and the possibility of its adaptation to the object of research. Considering the presence of an ultra-wide band and miniature dimensions, the antenna can be a sensor of a multi-frequency multi-channel microwave radiothermograp

Correlation between binding rate constants and individual information of E. coli Fis binding sites

Individual protein binding sites on DNA can be measured in bits of information. This information is related to the free energy of binding by the second law of thermodynamics, but binding kinetics appear to be inaccessible from sequence information since the relative contributions of the on- and off-rates to the binding constant, and hence the free energy, are unknown. However, the on-rate could be independent of the sequence since a protein is likely to bind once it is near a site. To test this, we used surface plasmon resonance and electromobility shift assays to determine the kinetics for binding of the Fis protein to a range of naturally occurring binding sites. We observed that the logarithm of the off-rate is indeed proportional to the individual information of the binding sites, as predicted. However, the on-rate is also related to the information, but to a lesser degree. We suggest that the on-rate is mostly determined by DNA bending, which in turn is determined by the sequence information. Finally, we observed a break in the binding curve around zero bits of information. The break is expected from information theory because it represents the coding demarcation between specific and nonspecific binding

Creation of Structural Polymer Composite Materials for Functional Application Using Physicochemical Modification

The various aspects of physico-chemical modification of the components of structural materials of functional application based on classical composites and nanocomposites are analyzed. Potential applications of such materials are briefly described. Ultrasonic cavitation treatment is considered as a basic method of physical modification when obtaining the indicated classes of composites. The influence of ultrasonic treatment modes on the technological and operational properties of reactoplastic polymers, as well as on the hardening of reinforced composites based on them, is investigated. Technical means of ultrasonic cavitation processing of liquid binders and polymer composites based on them are briefly described. An effective spectrum of interrelated structural and technological parameters of ultrasonic treatment has been characterized, which is established by calculation and experimentally-statistically. The design issues of the technological processes of obtaining polymer composites of functional application are analyzed. The efficiency of creating carbon fiber composite materials, as well as the prospects for creating of these materials based on reinforcing fabric with nanomodified fillers is described. The methods of obtaining functional nanomodified carbon-composites with improved physicomechanical and operational properties, in particular with increased strength and electrical conductivity, are characterized. The effectiveness of the ultrasonic treatment and production of nanomodified thermoplastic composite materials by extrusion method is considered. Some issues of forming products from intelligent polymer composites are analyzed. The results of the survey can be used in the design of advanced technologies for the creation of functional polymer composites of functional application

Pilot studies of age-related changes in blood perfusion in two different types of skin

Laser Doppler flowmetry (LDF) was utilized to assess age-related changes in the blood microcirculation at the skin sites with different morphology and regulation. The LDF signals obtained from the glabrous skin of the middle finger pad and nonglabrous skin on the dorsal wrist surface were analyzed. Statistically higher baseline perfusion was observed in the zone with glabrous skin in the older group of volunteers compared to younger participants. Observed site-specific and age-related differences in perfusion can be used in the future experimental design for the studies of the blood microcirculation system in patients with different pathologies

Use of Physicochemical Modification Methods for Producing Traditional and Nanomodified Polymeric Composites with Improved Operational Properties

Various aspects of the methods of physical and physicochemical modification of components of filled thermo-plastic composite materials are analyzed, aimed at improving the surface properties of the fillers and the technological properties of the polymer matrix during their interaction. It is noted that the improvement of the interfacial interaction of the components of polymer reactoplastic composites, including adhesive strength, is a key factor for improving the reliability of the cured filled composite. As a promising area of research, a modification of the surface of the reinforcing fibrous filler and the technological characteristics of the liquid polymer binder, aimed at increasing their contact properties in the composite was chosen. The effectiveness of the physical method of modifying the components of composites in the form of low-frequency ultrasonic processing is described. The peculiarities of cluster formation and physicochemical modification of epoxy polymers filled with dispersed fillers are analyzed. Attention is focused on the effectiveness of ultrasonic processing in cavitation mode for deagglomeration and uniform distribution of nanoparticles in a liquid medium during the creation of nanocomposites. Experimentally confirmed the improvement of the technological properties of liquid epoxy polymers, modified by ultrasound, used for the impregnation of oriented fibrous fillers, as well as the improvement of the physicomechanical properties of the sonicated epoxy matrices

Wearable laser Doppler sensors for evaluating the nutritive and shunt blood flow

This study is devoted to the trials of wearable diagnostic system that implements the laser Doppler flowmetry technique to analyse the blood microcirculation. We do preliminary test with involvement of limited group of healthy volunteers of different age and in patients with type 2 diabetes. During the series of measurements, the microcirculation parameters was measured for 10 minutes in the palmar surfaces of the big toes and in the inner sides of the upper thirds of the shins. A statistically significant differences was found in bypass index, nutritive and shunt blood ow in shins between older group of volunteers and patients' group as well as in shunt blood flow in fingers between younger and older groups of volunteers

Studies of age-related changes in blood perfusion coherence using wearable blood perfusion sensor system

Laser Doppler flowmetry (LDF) was used for detection of age-related changes in the blood microcirculation. The LDF signal was simultaneously recorded from the 3rd fingers' pads of both hands. Amplitudes of the blood flow oscillations and wavelet coherence of the signals were used for the data analysis. A statistical difference in the synchronisation of myogenic oscillations was found between the two studied age groups. Myogenic oscillations of blood perfusion in the younger group had a higher wavelet coherence parameter than in the older group. Observed site-specific and age-related differences in blood perfusion can be used in the future in the design of experimental studies of the blood microcirculation system in patients with different pathologies