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Of all publications in the section: 652
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Article
Permogorskiy M. S. Biology Bulletin Reviews. 2015. Vol. 5. No. 3. P. 213-219.
The contemporary state of the competitive intransitivity hypothesis is considered. Intransitive competition among species occurs when, for example, species A outcompetes species B, B outcompetes C, and C outcompetes A (sometimes written as A > B > C > A). In the first part of the article, a summary of the studies of competitive intransitivity is given. Examples of actually existing intransitive loops, as well as simulation models that provide a theoretical explanation for these processes, are discussed. For competitive intransitivity to emerge, it is necessary (but is it enough?) that the community has sufficient potential diver sity, that species interactions are carried out in a relatively stable limited space, and that there is a penalty for the acquisition of competitive ability. In the second part, the competitive intransitivity hypothesis is compared with neutral theory and niche theory. The results are believed to make it possible to form some generalizations, which could stimulate a deeper understanding of the species coexistence phenomenon.
Added: Jul 13, 2015
Article
Ossadtchi A. Journal of Neuroscience Methods. 2012. Vol. 207. No. 1. P. 1-16.

Connectivity measures are (typically bivariate) statistical measures that may be used to estimate interactions between brain regions from electrophysiological data. We review both formal and informal descriptions of a range of such measures, suitable for the analysis of human brain electrophysiological data, principally electro- and magnetoencephalography. Methods are described in the space–time,space–frequency, and space–time–frequency domains. Signal processing and information theoretic measures are considered, and linear and nonlinear methods are distinguished. A novel set of crosstime–frequency measures is introduced, including a cross-time–frequency phase synchronization measure.

Added: Oct 23, 2014
Article
Mazin P., Jiang X., Fu N. et al. RNA. 2018. P. 585-596.

Changes in splicing are known to affect the function and regulation of genes. We analyzed splicing events that take place during the postnatal development of the prefrontal cortex in humans, chimpanzees, and rhesus macaques based on data obtained from 168 individuals. Our study revealed that among the 38,822 quantified alternative exons, 15% are differentially spliced among species, and more than 6% splice differently at different age. Mutations in splicing acceptor and/or donor sites might explain more than 14% of all splicing differences among species and up to 64% of high-amplitude differences. A reconstructed trans- regulatory network containing 21 RNA-binding proteins explain a further 4% of splicing variations within species. While most age-dependent splicing patterns are conserved among the three species, developmental changes in intron retention are substantially more pronounced in humans.

Added: Mar 5, 2018
Article
Poptsova M., Grechishnikova D. BMC Genomics. 2016. Vol. 17. No. 1. P. 992.

Abstract BACKGROUND:

In the process of retrotransposition LINEs use their own machinery for copying and inserting themselves into new genomic locations, while SINEs are parasitic and require the machinery of LINEs. The exact mechanism of how a LINE-encoded reverse transcriptase (RT) recognizes its own and SINE RNA remains unclear. However it was shown for the stringent-type LINEs that recognition of a stem-loop at the 3'UTR by RT is essential for retrotransposition. For the relaxed-type LINEs it is believed that the poly-A tail is a common recognition element between LINE and SINE RNA. However polyadenylation is a property of any messenger RNA, and how the LINE RT recognizes transposon and non-transposon RNAs remains an open question. It is likely that RNA secondary structures play an important role in RNA recognition by LINE encoded proteins.

RESULTS:

Here we selected a set of L1 and Alu elements from the human genome and investigated their sequences for the presence of position-specific stem-loop structures. We found highly conserved stem-loop positions at the 3'UTR. Comparative structural analyses of a human L1 3'UTR stem-loop showed a similarity to 3'UTR stem-loops of the stringent-type LINEs, which were experimentally shown to be recognized by LINE RT. The consensus stem-loop structure consists of 5-7 bp loop, 8-10 bp stem with a bulge at a distance of 4-6 bp from the loop. The results show that a stem loop with a bulge exists at the 3'-end of Alu. We also found conserved stem-loop positions at 5'UTR and at the end of ORF2 and discuss their possible role.

CONCLUSIONS:

Here we presented an evidence for the presence of a highly conserved 3'UTR stem-loop structure in L1 and Alu retrotransposons in the human genome. Both stem-loops show structural similarity to the stem-loops of the stringent-type LINEs experimentally confirmed as essential for retrotransposition. Here we hypothesize that both L1 and Alu RNA are recognized by L1 RT via the 3'-end RNA stem-loop structure. Other conserved stem-loop positions in L1 suggest their possible functions in protein-RNA interactions but to date no experimental evidence has been reported.

 

Added: Mar 8, 2017
Article
Daryin A., Alexandrin M., Grachev A. et al. Bulletin of the Russian Academy of Sciences: Physics. 2019. Vol. 83. No. 2. P. 190-193.

Cores of bottom sediments of Lake Karakel (Northern Caucasus) were obtained in 2010 and 2014 to perform geochemical studies for reconstructing the regional paleoclimate of the late Holocene. Solid sam- ples of bottom sediments were scanned via micro-XRF with a step of 1 mm at the shared resource center of the Siberian Synchrotron and Terahertz Radiation Center. The contents of more than 20 elements were deter- mined. The scan profiles are used to construct a single reference section with correction for a sediment layer dated via radiocarbon analysis, and to create a sediment core age–depth model.

Added: Oct 23, 2019
Article
Mazin P., Gelfand M. S. Proceedings of the National Academy of Sciences of the United States of America. 2018. P. E2477-E2486.

Polypedilum vanderplanki is a striking and unique example of an insect that can survive almost complete desiccation. Its genome and a set of dehydration-rehydration transcriptomes, together with the genome of Polypedilum nubifer (a congeneric desiccation-sensitive midge), were recently released. Here, using published and newly generated datasets reflecting detailed transcriptome changes during anhydrobiosis, as well as a developmental series, we show that the TCTAGAA DNA motif, which closely resembles the binding motif of the Drosophila melanogaster heat shock transcription activator (Hsf), is significantly enriched in the promoter regions of desiccation-induced genes in P. vanderplanki, such as genes encoding late embryogenesis abundant (LEA) proteins, thioredoxins, or trehalose metabolism-related genes, but not in P. nubifer Unlike P. nubiferP. vanderplanki has double TCTAGAA sites upstream of the Hsf gene itself, which is probably responsible for the stronger activation of Hsf in P. vanderplanki during desiccation compared with P. nubifer To confirm the role of Hsf in desiccation-induced gene activation, we used the Pv11 cell line, derived from P. vanderplanki embryo. After preincubation with trehalose, Pv11 cells can enter anhydrobiosis and survive desiccation. We showed that Hsf knockdown suppresses trehalose-induced activation of multiple predicted Hsf targets (including P. vanderplanki-specific LEA protein genes) and reduces the desiccation survival rate of Pv11 cells fivefold. Thus, cooption of the heat shock regulatory system has been an important evolutionary mechanism for adaptation to desiccation in P. vanderplanki.

Added: Mar 5, 2018
Article
Dubois J., Kulikova S., Hertz-Pannier L. et al. Magnetic Resonance Imaging. 2014. Vol. 32. No. 8. P. 981-992.
Objective

Diffusion imaging techniques such as DTI and HARDI are difficult to implement in infants because of their sensitivity to subject motion. A short acquisition time is generally preferred, at the expense of spatial resolution and signal-to-noise ratio. Before estimating the local diffusion model, most pre-processing techniques only register diffusion-weighted volumes, without correcting for intra-slice artifacts due to motion or technical problems. Here, we propose a fully automated strategy, which takes advantage of a high orientation number and is based on spherical-harmonics decomposition of the diffusion signal.

Material and methods

The correction strategy is based on two successive steps: 1) automated detection and resampling of corrupted slices; 2) correction for eddy current distortions and realignment of misregistered volumes. It was tested on DTI data from adults and non-sedated healthy infants.

Results

The methodology was validated through simulated motions applied to an uncorrupted dataset and through comparisons with an unmoved reference. Second, we showed that the correction applied to an infant group enabled to improve DTI maps and to increase the reliability of DTI quantification in the immature cortico-spinal tract.

Conclusion

This automated strategy performed reliably on DTI datasets and can be applied to spherical single- and multiple-shell diffusion imaging.

Added: Oct 22, 2015
Article
Vukovic N., Shtyrov Y. Neuroimage. 2014. Vol. 102. No. P2. P. 695-703.

Understanding neurocognitive mechanisms supporting the use of multiple languages is a key question in language science. Recent neuroimaging studies in monolinguals indicated that core language areas in human neocortex together with sensorimotor structures form a highly interactive system underpinning native language comprehension. While the experience of a native speaker promotes the establishment of strong action-perception links in the comprehension network, this may not necessarily be the case for L2 where, as it has been argued, the most a typical L2 speaker may get is a link between an L2 wordform and its L1 translation equivalent. Therefore, we investigated, whether the motor cortex of bilingual subjects shows differential involvement in processing action semantics of native and non-native words. We used high-density EEG to dynamically measure changes in the cortical motor system's activity, indexed by event-related desynchronisation (ERD) of the mu-rhythm, in response to passively reading L1 (German) and L2 (English) action words. Analysis of motor-related EEG oscillations at the sensor level revealed an early (starting ~150ms) and left-lateralised coupling between action and semantics during both L1 and L2 processing. Crucially, source-level activation in the motor areas showed that mu-rhythm ERD, while present for both languages, is significantly stronger for L1 words. This is the first neurophysiological evidence of rapid motor-cortex involvement during L2 action-semantic processing. Our results both strengthen embodied cognition evidence obtained previously in monolinguals and, at the same time, reveal important quantitative differences between L1 and L2 sensorimotor brain activity in language comprehension.

Added: Oct 23, 2014
Article
Butovskaya M. Frontiers in Psychology. 2017. Vol. 8. No. 1427. P. 1-6.

Previous research documents that men and women can accurately judge male physical strength from gait, but also that the sexes differ in attractiveness judgments of strong and weak male walkers. Women’s (but not men’s) attractiveness assessments of strong male walkers are higher than for weak male walkers. Here, we extend this research to assessments of strong and weak male walkers in Chile, Germany, and Russia. Men and women judged videos of virtual characters, animated with the walk movements of motion-captured men, on strength and attractiveness. In two countries (Germany and Russia), these videos were additionally presented at 70% (slower) and 130% (faster) of their original speed. Stronger walkers were judged to be stronger and more attractive than weak walkers, and this effect was independent of country (but not sex). Women tended to provide higher attractiveness judgments to strong walkers, and men tended to provide higher attractiveness judgments to weak walkers. In addition, German and Russian participants rated strong walkers most attractive at slow and fast speed. Thus, across countries men and women can assess male strength from gait, although they tended to differ in attractiveness assessments of strong and weak male walkers. Attractiveness assessments of male gait may be influenced by society-specific emphasis on male physical strength.

Added: Feb 19, 2018
Article
Nikulin V., Nolte G., Curio G. Clinical Neurophysiology. 2012. Vol. 7. No. 123. P. 1353-1360.

OBJECTIVE:

We present a novel method for the extraction of neuronal components showing cross-frequency phase synchronization.

METHODS:

In general the method can be applied for the detection of phase interactions between components with frequencies f1 and f2, where f2 ≈ rf1 and r is some integer. We refer to the method as cross-frequency decomposition (CFD), which consists of the following steps: (a) extraction of f1-oscillations with the spatio-spectral decomposition algorithm (SSD); (b) frequency modification of the f1-oscillations obtained with SSD; and (c) finding f2-oscillations synchronous with f1-oscillations using least-squares estimation.

RESULTS:

Our simulations showed that CFD was capable of recovering interacting components even when the signal-to-noise ratio was as low as 0.01. An application of CFD to the real EEG data demonstrated that cross-frequency phase synchronization between alpha and beta oscillations can originate from the same or remote neuronal populations.

CONCLUSIONS:

CFD allows a compact representation of the sets of interacting components. The application of CFD to EEG data allows differentiating cross-frequency synchronization arising due to genuine neurophysiological interactions from interactions occurring due to quasi-sinusoidal waveform of neuronal oscillations.

SIGNIFICANCE:

CFD is a method capable of extracting cross-frequency coupled neuronal oscillations even in the presence of strong noise.

Copyright © 2011 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

 

Added: Oct 23, 2014
Article
Derkachev P. Russian Education and Society. 2015. Vol. 57. No. 7. P. 572-589.

This paper presents an overview of studies on the correlations of teacher pay to regional economics and to regional factors affecting the size of teacher salaries. It describes the basic pay indicators for teachers in the regions: absolute salary, teacher pay level as compared to the average regional salary, and ratio of salary to the cost of a fixed set of goods and services and to the per capita gross regional product. Based on calculations that used open government databases, a classification of regions by teacher pay level was developed. Regions of the country turned out to belong to seven different clusters. Recommendations on teacher remuneration were developed for each of these clusters and common risks and challenges were identified.

Added: Mar 7, 2018
Article
Garlitska L., Neretina T. V., Schepetov DImitry et al. Molecular Ecology. 2012. No. 21. P. 5336-5347.

Nannopus palustris Brady, 1880 is a free-living widely distributed harpacticoid copepod, which has been formerly assumed to be a single, cosmopolitan but highly variable species. We compared several geographically distant N. palustris populations in terms of their morphology and genetics. Populations from the White Sea (WS), the North Sea (NS), the Black Sea (BS) and two sympatric morphs from South Carolina, USA (SC notched and SC straight morphs), were considered. The NS, BS and to a lesser extent SC notched specimens were morphologically similar and partly coincided to the ‘canonical’ description of the species. By contrast, WS population showed remark able anatomical and morphometric peculiarities that correspond to some earlier descriptions. Genetic analyses of mitochondrial (cytochrome b) and nuclear (28S rDNA) genes demonstrated the significant distinctness among WS, both SC and (NS+BS) populations, the latter two being genetically indistinguishable. Concordance between mitochondrial and nuclear gene trees and morphological data supports that N. palustris is in fact composed of several pseudo-sibling species, which are genetically and morphologically divergent. Neither correlation between genetic divergence and geographical distance nor significant intrapopulation diversity was found for these species. Taxonomic status, distribution and phylogenetic relationships of the species within the Nannopus genus need to be reconsidered. A further subdivision of species complexes might have important implications for the analysis of biodiversity of benthic copepods and consequently for the interpretation of their (species-specific) ecological function.

Added: Oct 19, 2014
Article
Kuzmenkov A., Peigneur S., Chugunov A. et al. Biochimica et Biophysica Acta - Proteins and Proteomics. 2017. Vol. 1865. P. 465-472.

We report isolation, sequencing, and electrophysiological characterization of OSK3 (α-KTx 8.8 in Kalium and Uniprot databases), a potassium channel blocker from the scorpion Orthochirus scrobiculosus venom. Using the voltage clamp technique, OSK3 was tested on a wide panel of 11 voltage-gated potassium channels expressed in Xenopus oocytes, and was found to potently inhibit Kv1.2 and Kv1.3 with IC50 values of ~ 331 nM and ~ 503 nM, respectively. OdK1 produced by the scorpion Odontobuthus doriae differs by just two C-terminal residues from OSK3, but shows marked preference to Kv1.2. Based on the charybdotoxin-potassium channel complex crystal structure, a model was built to explain the role of the variable residues in OdK1 and OSK3 selectivity.

Added: Mar 14, 2017
Article
Zelenyi L., Malova H., Grigorenko E. et al. Plasma Physics and Controlled Fusion. 2019. Vol. 61. P. 1-12.

In this article we aim to highlight the problems related to the structure and stability of the comparatively thin current sheets that were relatively recently discovered by space missions in the magnetospheres of the Earth and planets, as well as in the solar wind. These magnetoplasma structures are universal in collisionless cosmic plasmas and can play a key role in the processes of storage and release of energy in the space environment. The development of a self-consistent theory for these sheets in the Earth’s magnetosphere, where they were first discovered, has a long and dramatic history. Solution of the problem of the thin current sheet structure and stability become possible in the framework of a kinetic quasi-adiabatic approach required to explain their embedding and metastability properties. It was found that the structure and stability of current structures are completely determined by the nonlinear dynamics of plasma particles. Theoretical models have been developed to predict many properties of these structures and interpret many experimental observations in planetary magnetospheres and the heliosphere.

Added: Mar 22, 2019
Article
Gerasimova K. Science and Engineering Ethics. 2016. Vol. 22. No. 2. P. 525-547.

The paper discusses conflicts in perceptions of GM crops illustrating the complexities of GM debates and applications of the concept of sustainable development. The concept consists of three discourses that both opponents and supporters of GM crops refer to in their analyses: environmentalism, social and economic development and the two sub-issues of sustainable development—biodiversity loss and food security. This creates a unique situation when both proponents and opponents of GM food use the same framework of sustainable development to support their arguments and do not reach a common ground. This will be illustrated by a review of the arguments brought by these two groups.

Added: Aug 1, 2017
Article
Liliya Karachurina. Regional Research of Russia. 2014. Vol. 4. No. 2. P. 56-67.

The dynamics of the system of cities in Russia in 1989–2010 is analyzed based on the population census data in 1989, 2002, and 2010, as well as the current population register. The extent of the decline or less often of the increase of the population size are considered for cities of different sizes for each intercensal period (1989–2002 and 2002–2010) and factors contributing to this are noted. The change in the populationsize of cities is analyzed, depending on their size and geographical location, expressed in the distance to the center of the federal subject. It turned out that in the 1990s and in the 2000s, the population of cities of different sizes, but located at a distance of up to 50 km from the regional center increased, and at greater distances the dynamics were not so welldefined. The dependence of the growth/decline of the population of cities on their size is more variable: the population of cities of different sizes both grew and declined. The dynamics of the natural increase and migration increase of cities with different sizes of population show that the higher the population size the greater the importance of migration increase as a compensator of natural decrease.

Added: Oct 16, 2014
Article
Borodovsky M., Peresetsky A. Computers and Chemistry. 1994. Vol. 18. No. 3. P. 259-268.

Non-homogeneous Markov chain models can represent biologically important regions of DNA sequences. The statistical pattern that is described by these models is usually weak and was found primarily because of strong biological indications. The general method for extracting similar patterns is presented in the current paper. The algorithm incorporates cluster analysis, multiple alignment and entropy minimization. The method was first tested using the set of DNA sequences produced by Markov chain generators. It was shown that artificial gene sequences, which initially have been randomly set up along the multiple alignment panels, are aligned according to the hidden triplet phase. Then the method was applied to real protein-coding sequences and the resulting alignment clearly indicated the triplet phase and produced the parameters of the optimal 3-periodic non-homogeneous Markov chain model. These Markov models were already employed in the GeneMark gene prediction algorithm, which is used in genome sequencing projects. The algorithm can also handle the case in which the sequences to be aligned reveal different statistical patterns, such as Escherichia co/i protein-coding sequences belonging to Class II and Class III. The algorithm accepts a random mix of sequences from different classes, and is able to separate them into two groups (clusters), align each cluster separately, and define a non-homogeneous Markov chain model for each sequence cluster.

Added: Apr 20, 2018
Article
Dabek J., Nikulin V., Ilmoniemi R. Journal of Neuroscience Methods. 2014. No. 235. P. 10-24.

Background

The spatiotemporal coupling of brainwaves is commonly quantified using the amplitude or phase of signals measured by electro- or magnetoencephalography (EEG/MEG). To enhance the temporal resolution for coupling delays down to millisecond level, a new power correlation (PC) method is proposed and tested.

New method

The cross-correlations of any two brainwave powers at two locations are calculated sequentially through a measurement using the convolution theorem. For noise suppression, the cross-correlation series is moving-average filtered, preserving the millisecond resolution in the cross-correlations, but with reduced noise. The coupling delays are determined from the delays of the cross-correlation peaks.

Results

Simulations showed that the new method detects reliably power cross-correlations with millisecond accuracy. Moreover, in MEG measurements on three healthy volunteers, the method showed average alpha–alpha coupling delays of around 0–20 ms between the occipital areas of two hemispheres. Lower-frequency brainwaves vs. alpha waves tended to have a larger lag; higher-frequency waves vs. alpha waves showed delays with large deviations.

Comparison with existing methods

The use of signal power instead of its square root (amplitude) in the cross-correlations improves noise cancellation. Compared to signal phase, the signal power analysis time delays do not have periodic ambiguity. In addition, the novel method allows fast calculation of cross-correlations.

Conclusions

The PC method conveys novel information about brainwave dynamics. The method may be extended from sensor-space to source-space analysis, and can be applied also for electroencephalography (EEG) and local field potentials (LFP).

Added: Oct 23, 2014
Article
Kalinina A., Suvorikova A., Spokoiny V. et al. Journal of Bioinformatics and Computational Biology. 2016. Vol. 14. No. 2. P. 1641001-1-1641001-12.

Detection of recombination events in a bacterial genome is both important from the evolutionary point of view, and of practical interest. Indeed, homologous recombination (HR) plays a major role in the exchange of antigenic determinants between strains. There exist statistical methods to detect recently recombined segments in whole-genome sequences that use a high local density of substitutions as a signal of HR events with a source outside considered strains. However, it is difficult to detect the HR events within a set of strains, which represent whole species diversity, due to a low number of substitutions in recombined segments and high level of diversity of strains. Here, we analyzed HR in 20 Escherichia coli (E. coli) strains to define what fraction of segments with a high substitution rate were introduced in a genome by HR. For detection of HR, we used the segmentation, performed by the adaptive weights smoothing (AWS) algorithm. It detects sharp changes in the structure of observed data analyzing only qualitative structural information. We validated the approach on simulated data, applied it to the analysis of E. coli strains, and determined the recombination rates between phylogroups.

Added: Mar 13, 2017
Article
Hardstone R., Poil S., Schiavone G. et al. Frontiers in Psychology. 2012. No. 3. P. 450.

Recent years of research have shown that the complex temporal structure of ongoing oscillations is scale-free and characterized by long-range temporal correlations. Detrended fluctuation analysis (DFA) has proven particularly useful, revealing that genetic variation, normal development, or disease can lead to differences in the scale-free amplitude modulation of oscillations. Furthermore, amplitude dynamics is remarkably independent of the time-averaged oscillation power, indicating that the DFA provides unique insights into the functional organization of neuronal systems. To facilitate understanding and encourage wider use of scaling analysis of neuronal oscillations, we provide a pedagogical explanation of the DFA algorithm and its underlying theory. Practical advice on applying DFA to oscillations is supported by MATLAB scripts from the Neurophysiological Biomarker Toolbox (NBT) and links to the NBT tutorial website http://www.nbtwiki.net/. Finally, we provide a brief overview of insights derived from the application of DFA to ongoing oscillations in health and disease, and discuss the putative relevance of criticality for understanding the mechanism underlying scale-free modulation of oscillations.

Added: Oct 23, 2014
Article
Ivlev N., Ovchinnikov M. Y., Ivanov D. et al. Acta Astronautica. 2014. Vol. 93. P. 23-33.

The key-problems of design, examination, laboratory' and flight testing of the attitude determination and control system (ADCS) dedicated for a microsatellite arc considered. The system consists of three pairs of the reaction wheels, three magnetorquers, set of Sun sensors, three-axis magnetometer and a control unit. ADCS, on one hand, is subjected to the high accuracy and reliability requirements, and, on the other hand, power consumption, total mass and volume limitations. It is meant for the LEO satellite with mass between 10 and 50 kg. The problems are solved within several steps, i.e. preliminary study of the satellite dynamics using asymptotical and numerical techniques, hardware and software design, testing of each actuator and sensor and the whole ACS on the test-bench dedicated specially for such a laboratory simulation. Finally flight testing has been carried out to validate ADCS functioning. In this paper both dynamics of the microsatellite with ADCS and mock-up of ADCS operation are studied. Reaction wheels control law parameters are chosen to provide the maximum degree of stability. The evolution of the reaction wheels angular momentum is also studied and the problem of the desaturation with use of the magnetorquers is solved. Attitude accuracy is estimated in terms of closed-form formulae. Some aspects of in-flight ADCS exploitation onboard the Russian microsatellite "Chibis-M" developed, designed and fabricated by the Institute of Space Research of RAS and orbited from SC "Progress" on 25th of January, 2012 are presented. Flight showed a good correspondence between analytical, numerical and laboratory' study with in-flight testing.

Added: Jun 8, 2018