Institute for Information Transmission Problems Kharkevich Institute

Moscow, Russia

Institute for Information Transmission Problems Kharkevich Institute

Moscow, Russia

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Kurmangaliyev Y.Z.,University of Southern California | Kurmangaliyev Y.Z.,Institute for Information Transmission Problems Kharkevich Institute | Favorov A.V.,Johns Hopkins University | Favorov A.V.,Vavilov Institute of General Genetics | And 9 more authors.
BMC Genomics | Year: 2015

Background: Variation within splicing regulatory sequences often leads to differences in gene models among individuals within a species. Two alleles of the same gene may express transcripts with different exon/intron structures and consequently produce functionally different proteins. Matching genomic and transcriptomic data allows us to identify putative regulatory variants associated with changes in splicing patterns. Results: Here we analyzed natural variation of splicing patterns in the transcriptomes of 81 natural strains of Drosophila melanogaster with known genotypes. We identified dozens of genotype-specific splicing patterns associated with putative cis-splicing quantitative trait loci (sQTL). The majority of changes can be explained by mutations in splice sites. Allelic-imbalance in splicing patterns confirmed that the majority are regulated mainly by cis-genetic effects. Remarkably, allele-specific splicing changes often lead to qualitative changes in gene models, yielding many isoforms not previously annotated. The observed alterations are typically outside protein-coding regions or affect only very short protein segments. Conclusions: Overall, the sets of gene models appear to be flexible within D. melanogaster populations. The observed variation in splicing patterns are predicted to have limited effects on the encoded protein sequences. To our knowledge, this is the first sQTL mapping study in Drosophila. © Kurmangaliyev et al.


PubMed | Sloan Kettering Cancer Center, Johns Hopkins University, University of Southern California and Institute for Information Transmission Problems Kharkevich Institute
Type: | Journal: BMC genomics | Year: 2015

Variation within splicing regulatory sequences often leads to differences in gene models among individuals within a species. Two alleles of the same gene may express transcripts with different exon/intron structures and consequently produce functionally different proteins. Matching genomic and transcriptomic data allows us to identify putative regulatory variants associated with changes in splicing patterns.Here we analyzed natural variation of splicing patterns in the transcriptomes of 81 natural strains of Drosophila melanogaster with known genotypes. We identified dozens of genotype-specific splicing patterns associated with putative cis-splicing quantitative trait loci (sQTL). The majority of changes can be explained by mutations in splice sites. Allelic-imbalance in splicing patterns confirmed that the majority are regulated mainly by cis-genetic effects. Remarkably, allele-specific splicing changes often lead to qualitative changes in gene models, yielding many isoforms not previously annotated. The observed alterations are typically outside protein-coding regions or affect only very short protein segments.Overall, the sets of gene models appear to be flexible within D. melanogaster populations. The observed variation in splicing patterns are predicted to have limited effects on the encoded protein sequences. To our knowledge, this is the first sQTL mapping study in Drosophila.


Rozhkova G.I.,Institute for Information Transmission Problems Kharkevich Institute | Nikolaev P.P.,Institute for Information Transmission Problems Kharkevich Institute
Perception | Year: 2015

A thorough analysis of the literature on retinal image stabilization, as well as our own experimental data, present evidence that Yarbus’s concept, implying inevitable and irreversible fading of a visible image evoked by stabilized retinal stimulus of any size, color, and luminance in 1 to 3 s after its onset, is not valid in a general case. It has been demonstrated that, even with Yarbus’s stabilization techniques, the lifetime of visible images varies from fractions of a second to the whole stimulus duration—up to 30 min in our experiments—depending on many factors: monocular or binocular viewing, stimulus parameters, characteristics of subjects, and so forth. The dynamics of perceived images is determined mainly by the processes at the higher levels of the visual system. In the cases of such unusual visual stimuli as stabilized retinal images, it is problematic for the visual brain to find their proper interpretations in terms of everyday natural experience. Usually, the responses of retinal units are determined by three types of coexisting images: (a) the optical projections of external objects, (b) shadows of the blood vessels and other internal eye structures, (c) virtual patterns caused by the traces of previous stimuli. A task of the visual system is to recognize and visualize only external objects separating their projections from all the entoptic images of the two remaining types. To implement separation, visual brain employs a number of approaches—in particular, the eye movements that cause sliding over the retina but only the projection of the external objects. This means that the peculiar phenomena observed in the cases of stabilized retinal images can be determined not by invariability of such stimuli per se but rather by the fact that stabilization eliminates a powerful cue helping to identify the retinal images belonging to the external objects, thereby increasing the probability to treat them as the entoptic ones which should be ignored or canceled rather than perceived. However, the probability of canceling—image fading—can be essentially reduced in conditions of concordant, large, bright, and sharp binocular stimuli. © 2015, © The Author(s) 2015.


Fedonin G.G.,Institute for Information Transmission Problems Kharkevich Institute | Rakhmaninova A.B.,Moscow State University | Korostelev Y.D.,Moscow State University | Laikova O.N.,Institute for Information Transmission Problems Kharkevich Institute | Gelfand M.S.,Institute for Information Transmission Problems Kharkevich Institute
Molecular Biology | Year: 2011

We studied 1372 LacI-family transcription factors and their 4484 DNA binding sites using machine learning algorithms and feature selection techniques. The Naive Bayes classifier and Logistic Regression were used to predict binding sites given transcription factor sequences and to classify factor-site pairs on binding and non-binding ones. Prediction accuracy was estimated using 10-fold cross-validation. Experiments showed that the best prediction of nucleotide densities at selected site positions is obtained using only a few key protein sequence positions. These positions are stably selected by the forward feature selection based on the mutual information of factor-site position pairs. © 2011 Pleiades Publishing, Ltd.


Merinov P.,Institute for Information Transmission Problems Kharkevich Institute | Belyaev M.,Institute for Information Transmission Problems Kharkevich Institute | Krivov E.,Institute for Information Transmission Problems Kharkevich Institute
Proceedings - 2015 International Conference on Biomedical Engineering and Computational Technologies, SIBIRCON 2015 | Year: 2015

One of the key objectives of brain-computer interface (BCI) design is to construct accurate electroencephalogram (EEG) based classifier. But out of laboratory all EEG signals are contaminated with artifacts, which hamper algorithmic processing and EEG analysis, i.e. classifier ought to get a prediction for noisy data. Real-time BCI system rely on relatively clean EEG signals. Therefore, the exclusion of artifacts is of special interest for BCI applications in everyday life. There are two main approaches to this objective: automatic EEG artifact rejection methods (subtract the noisy component) and robust classification methods (replace sensitive to outliers estimates with robust counterparts). The goal of this work is to quantitatively compare popular automatic EEG artifact rejection approaches with robust classification methods in terms of motor imagery (MI) classification paradigm. © 2015 IEEE.


Chervova L.S.,Moscow State University | Lapshin D.N.,Institute for Information Transmission Problems Kharkevich Institute
Journal of Ichthyology | Year: 2011

An original behavioral test was used to study the effect of opioid substances on the thresholds of nociceptive responses to pain stimuli-a series of electric impulses applied to nerve endings of the caudal fin-in the common carp (Cyprinus carpio). The substances tested included tramadol (μ-agonist of opioid receptors), DADLE (δ-agonist), and U-50488 (κ-agonist) injected intramuscularly in concentrations 10-100 nmol/g of body weight. Raised thresholds of sensitivity to the pain stimulus were observed in the studied fish 5 to 15 min after the injection. The degree of analgesia and the rate of its increase varied depending on the dose. The total duration of analgesia was 40 to 90 min and depended on the concentration of the injected substance. It was observed in some experiments that the analgesic effect of tramadol (the most efficient of the analgesics used) could last longer than 4 h. The analgesic effect of opioids was not detected in experiments where they were applied together with naloxone, an antagonist of opioids. Decreased motor response to pain stimuli after injections of analgesics was not caused by the immobilization of the animal, because the tested fish individuals released into an aquarium demonstrated normal swimming and their usual behavior. We concluded that the systems of opioid nociceptive regulation function similarly in fish and land vertebrates. This regulation can play an important role in defense behavior and in other behaviors in fish. © 2011 Pleiades Publishing, Ltd.


Malyar N.L.,Moscow Institute of Physics and Technology | Maximova E.V.,Moscow Institute of Physics and Technology | Talis V.L.,Institute for Information Transmission Problems Kharkevich Institute
Zhurnal Vysshei Nervnoi Deyatelnosti Imeni I.P. Pavlova | Year: 2016

Wfe analyzed kinematics of stair ascent and descent in autistic children and adolescents in comparison with age-matched healthy children and adolescents. Eight healthy adolescents, 6 autistic adolescents, 7 healthy children and 6 autistic children participated in the study. Ws found that autistic subjects of both groups showed significantly more fluctuations of hip joint angular velocity than age-matched control subjects while preparing for stair ascent. During preparation for stair descent these velocity fluctuations appeared mainly in autistic adolescents, moreover, autistic children exhibited less velocity fluctuations than children in control group while preparing for stair descent. The kinematics of the movement itself demonstrated significantly less hip abduction in both autistic children and adolescents than in age-matched controls during stair ascent, and less ankle joint plantar extension in autistic adolescents than in healthy adolescents during stair descent. Ws suppose that age-related changes in kinematics of leg motion during stair ascent and descent in autistic patients indicate aggravated motor coordination in autistic adolescents as compared with both healthy adolescents and autistic children.


PubMed | Institute for Information Transmission Problems Kharkevich Institute
Type: Journal Article | Journal: Perception | Year: 2015

A thorough analysis of the literature on retinal image stabilization, as well as our own experimental data, present evidence that Yarbuss concept, implying inevitable and irreversible fading of a visible image evoked by stabilized retinal stimulus of any size, color, and luminance in 1 to 3s after its onset, is not valid in a general case. It has been demonstrated that, even with Yarbuss stabilization techniques, the lifetime of visible images varies from fractions of a second to the whole stimulus duration-up to 30min in our experiments-depending on many factors: monocular or binocular viewing, stimulus parameters, characteristics of subjects, and so forth. The dynamics of perceived images is determined mainly by the processes at the higher levels of the visual system. In the cases of such unusual visual stimuli as stabilized retinal images, it is problematic for the visual brain to find their proper interpretations in terms of everyday natural experience. Usually, the responses of retinal units are determined by three types of coexisting images: (a) the optical projections of external objects, (b) shadows of the blood vessels and other internal eye structures, (c) virtual patterns caused by the traces of previous stimuli. A task of the visual system is to recognize and visualize only external objects separating their projections from all the entoptic images of the two remaining types. To implement separation, visual brain employs a number of approaches--in particular, the eye movements that cause sliding over the retina but only the projection of the external objects. This means that the peculiar phenomena observed in the cases of stabilized retinal images can be determined not by invariability of such stimuli per se but rather by the fact that stabilization eliminates a powerful cue helping to identify the retinal images belonging to the external objects, thereby increasing the probability to treat them as the entoptic ones which should be ignored or canceled rather than perceived. However, the probability of canceling--image fading--can be essentially reduced in conditions of concordant, large, bright, and sharp binocular stimuli.

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