The software for interactive evaluation of mass spectra stability and reproducibility.

SUMMARY: Mass spectrometry (MS) methods are widely used for the analysis of biological and medical samples. Recently developed methods, such as DESI, REIMS and NESI allow fast analyses without sample preparation at the cost of higher variability of spectra. In biology and medicine, MS profiles are often used with machine learning (classification, regression, etc.) algorithms and statistical analysis, which are sensitive to outliers and intraclass variability. Here, we present spectra similarity matrix (SSM) Display software, a tool for fast visual outlier detection and variance estimation in mass spectrometric profiles. The tool speeds up the process of manual spectra inspection, improves accuracy and explainability of outlier detection, and decreases the requirements to the operator experience. It was shown that the batch effect could be revealed through SSM analysis and that the SSM calculation can also be used for tuning novel ion sources concerning the quality of obtained mass spectra. AVAILABILITY AND IMPLEMENTATION: Source code, example datasets, binaries and other information are available at https://github.com/EvgenyZhvansky/R_matrix. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

[Modification of the Rat Ethogram by Contagion Behavior].

The study was performed on a contagious behavior model based on drinking, behavior in rats. In the presence of familiar drink-motivated conspecific showing drinking behavior (rat-demonstrator), drink-unmotivated rat-viewer begins to demonstrate behavioral signs ofdrinking motivation that is the signs of behavioral contagion. In this paper; the changes in the ethogram of rats-viewers with behavioral contagion were studied by analyzing atransition probabilities matrix. Those animals showed a decrease in the frequency of aggression and defensive behavior patterns simultaneously with an increase in the frequency of exploratory activity, drinking and exploratory approaches to bottles as compared with the ethogram of rats-viewers with no signs of behavioral contagion when tested in the presence of familiar drink-unmotivated con specific-demonstrator.

[The contagious behavior model on the basis of rat drinking behavior].

In work, the attempt of contagious behavior modeling on the basis of rat drinking behavior was made. Rats' behavior was observed in home cage with two bottles. The rat without drinking motivation (viewer) was placed in the cage for adaptation. The rat-demonstrator was placed into the same cage 3 minutes later. If the viewer was tested with drink-motivated demonstrator, it had less latency of approach to bottles, higher frequency of approaches and increased drinking behavior time than the rat tested with unmotivated demonstrator or the rat tested without demonstrator. The intragastric infusion of coffee increased frequency of approaches to demonstrated bottle. Phenazepam intragastric injection decreased frequency of approaches and drinking behavior time at demonstrated bottle. The results suggest that drugs may affect rat contagious behavior based on drinking behavior.

[Effects of distorted geomagnetic field on the functioning of systems supporting rat's bone matrix adaptation and metabolism in open field].

Physiological responses of rats to daily 30-minute exposure to distorted geomagnetic field (DGMF) over 3 and 7 days and their reaction to open field following the exposure were studied. Increases in blood 11-oxycorticosteroids (11-OCS) were observed equally after 3- and 7-day DGMF exposure, whereas adrenal 11-OCS was found increased only on DGMF day-3; neither adrenaline in the adrenals nor glycogen in the liver were affected. On DGMF day-7, activation of bone matrix demineralization manifested itself by increased phosphorus and decreased calcium in blood, and activation of acidic phosphatase in serum. Rats reacted to open field by increases in blood and hepatic 11-OCS, reduction in adrenaline in the adrenals and glycogen in the liver, increase in serum free oxyproline and acidic phosphatase activation, and inhibition of alkaline phosphatase. Seven-day DGMF heightened or aggravated the reaction to open field.

Unified representation of high- and low-resolution spectra to facilitate application of mass spectrometric techniques in clinical practice.

The majority of research in the biomedical sciences is carried out with the highest resolution accessible to the scientist, but, in the clinic, cost constraints necessitate the use of low-resolution devices. Here, we compare high- and low-resolution direct mass spectrometry profiling data and propose a simple pre-processing technique that makes high-resolution data suitable for the development of classification and regression techniques applicable to low-resolution data, while retaining high accuracy of analysis. This work demonstrates an approach to de-noising spectra to make the same representation for both high- and low-resolution spectra. This approach uses noise threshold detection based on the Tversky index, which compares spectra with different resolutions, and minimizes the percentage of resolution-specific peaks. The presented method provides an avenue for the development of analytical algorithms using high-resolution mass spectrometry data, while applying these algorithms in the clinic using low-resolution mass spectrometers.

Activity and characterization of sialyltransferase from serum of normal rats, of rats bearing Zajdela ascitic hepatoma, in normal host liver and in Zajdela hepatoma cells.

Comparative studies on the content of sialic acid and on the sialyltransferase activity in normal serum and in serum of rats with Zajdela ascitic hepatoma in different phases of tumor development have been conducted. Unlike the serum from animals with tumors, in which the sialic acid quantity increases in dependence of the stage of tumor development, the activity of serum sialyltransferase statistically augmented only in serum of rats at the final stage of tumor progression. The sialyltransferase activity towards asialofetuin as an acceptor in normal liver and in Zajdela hepatoma cells, was measured and a decrease in this activity in tumor cells as well as in host liver was found. When lactose was used as acceptor, again lower enzyme activity in the tumor cells in comparison with that in liver was established, but in liver and in hepatoma cells the predominant 14C-labelled product of the sialyltransferase assay was alpha (2-6) sialyllactose isomer. The results contribute to the biochemical characterization of rat Zajdela hepatoma.