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Regular version of the site
Of all publications in the section: 600
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Article
Kulikova S., Abatis M., Heng C. et al. Cell Adhesion & Migration. 2011. Vol. 5. No. 4. P. 277-279.

A hallmark of neurogenesis in vertebrates is the apical-basal fluctuation of radial glia nuclei. Such a phenomenon, called INM, has been known for decades and is closely associated with mitosis but still puzzles scientists. An impressive step in the molecular understanding of INM has recently been achieved by Tsai and coworkers. Using RNA interference associated with time-lapse imaging, these authors demonstrated a dual motor system that can push/pull the nuclei accordingly with the cell cycle stages.

Added: Oct 22, 2015
Article
Grimshaw R., Pelinovsky E., Talipova T. et al. Nonlinear Processes in Geophysics. 2010. Vol. 17. No. 6. P. 633-649.

In coastal seas and straits, the interaction of barotropic tidal currents with the continental shelf, seamounts or sills is often observed to generate large-amplitude, horizontally propagating internal solitary waves. Typically these waves occur in regions of variable bottom topography, with the consequence that they are often modeled by nonlinear evolution equations of the Korteweg-de Vries type with
variable coecients. We shall review how these models are used to describe the propagation, deformation and disintegration of internal solitary waves as they propagate over the continental shelf and slope.

Added: Nov 19, 2012
Article
Kurichev N., Kuricheva E. K. Regional Science Policy and Practice. 2020.

The mutual influence of interregional migrations, the housing market, and the spatial transformation of the Moscow metropolitan area are studied empirically using the database of housing development projects and the depersonalized database of the residence addresses of buyers in the primary housing market. We consider the influence of natural rent, agglomeration economy, interregional inequality, and distance on the differentiation of the activity of residents of various Russian regions and cities in the primary housing market of the Moscow metropolitan area compared to their migration activity. The main characteristics of the extensive development of the Moscow metropolitan area are the prevalence of large greenfield residential district projects, urban sprawl in the near suburban zone, and the concentration of construction along transport corridors in the middle suburban zone. Selective influence of buyers from other regions on various zones of the Moscow metropolitan area owes to their orientation at the most affordable proposals in the primary market. The near suburban zone is the main gate into the Moscow metropolitan area for migrants, and construction in this zone is a major mechanism of restricting housing prices and maintaining economic incentives for large-scale migration to the Moscow region. Proceeding from the generalization of factors of the spatial transformation of the Moscow metropolitan area, a conceptual model of interaction between migration and urban spatial shifts is proposed.

Added: Oct 21, 2019
Article
Kononenko O., Vladimir Galatenko, Andersson M. et al. FASEB Journal. 2017.

Regulation of the formation and rewiring of neural circuits by neuropeptides may require coordinated production of these signaling molecules and their receptors that may be established at the transcriptional level. Here, we address this hypothesis by comparing absolute expression levels of opioid peptides with their receptors, the largest neuropeptide family, and by characterizing coexpression (transcriptionally coordinated) patterns of these genes. We demonstrated that expression patterns of opioid genes highly correlate within and across functionally and anatomically different areas. Opioid peptide genes, compared with their receptor genes, are transcribed at much greater absolute levels, which suggests formation of a neuropeptide cloud that covers the receptor-expressed circuits. Surprisingly, we found that both expression levels and the proportion of opioid receptors are strongly lateralized in the spinal cord, interregional coexpression patterns are side-specific, and intraregional coexpression profiles are affected differently by left- and right-side unilateral body injury. We propose that opioid genes are regulated as interconnected components of the same molecular system distributed between distinct anatomic regions. The striking feature of this system is its asymmetric coexpression patterns, which suggest side-specific regulation of selective neural circuits by opioid neurohormones.

Added: Mar 14, 2017
Article
Savina O. N., Bespalov P. A. Central European Astrophysical Bulletin. 2011. Vol. 35. No. 1. P. 83-91.

Within the framework of model calculations the possibility of occurrence of the ion-acoustic oscillation instability in a plasma without current and particle fluxes, but with an anisotropic distribution function, which corresponds to heat flux is shown. The model distribution function was selected taking into account the medium conditions. The increment of ion-acoustic oscillation is investigated as functional of the distribution function parameters. The threshold condition for the anisotropic part of the distribution function, under which the build-up of ion-acoustic oscillation with the wave vector opposite to the heat flux begins is studied. The critical heat flux, which corresponds to the threshold of ion-acoustic instability, is determined. For the solar conditions, the critical heat flux proved to be close to the heat flux from the corona into the chromosphere on the boundary of the transition region. The estimations show that outside of active regions and even in active regions with weaker magnetic fields ion-acoustic turbulence can be responsible for the formation of the sharp temperature jump. The generalized Wiedemann-Franz law for a non-isothermic quasi-neutral plasma with developed ion-acoustic turbulence is discussed. This law determines the relationship between electrical and thermal conductivities in a plasma with well-developed ion-acoustic turbulence. The anomalously low thermal conductivity responsible to the formation of high temperature gradients in the zone of the temperature jump is explained. The results are used to explain some properties of stellar atmosphere transition regions.

Added: Dec 12, 2012
Article
Kuzmenkov A., Krylov N., Chugunov A. et al. Database: the journal of biological databases and curation. 2016. Vol. 2016. No. baw056. P. 1-7.

Kalium ( http://kaliumdb.org/ ) is a manually curated database that accumulates data on potassium channel toxins purified from scorpion venom (KTx). This database is an open-access resource, and provides easy access to pages of other databases of interest, such as UniProt, PDB, NCBI Taxonomy Browser, and PubMed. General achievements of Kalium are a strict and easy regulation of KTx classification based on the unified nomenclature supported by researchers in the field, removal of peptides with partial sequence and entries supported by transcriptomic information only, classification of β-family toxins, and addition of a novel λ-family. Molecules presented in the database can be processed by the Clustal Omega server using a one-click option. Molecular masses of mature peptides are calculated and available activity data are compiled for all KTx. We believe that Kalium is not only of high interest to professional toxinologists, but also of general utility to the scientific community.

Database URL : http://kaliumdb.org/

Added: Mar 14, 2017
Article
Anosov S. E., Spiridonov V. A., Neretina T. V. et al. Polar Biology. 2015. Vol. 38. No. 2. P. 231-249.

In many areas of the Antarctic and Subantarctic, king crabs records are still fragmentary. New data on the distribution of Lithodidae in the Scotia Sea and the adjacent area of the south-west Atlantic and the south-east Pacific have been collected during exploratory pot fishing in the year 2010 and are also based on some earlier collections that are deposited in Russian museums. The occurrence of Lithodes macquariae off Peter I Island is confirmed. Lithodes confundens, Lithodes turkayi and Neolithodes diomedeae were found in abundance on the Northern Scotia Ridge at a depth of, respectively, 315–775, 315–1,410 and 840–1,300 m. Paralomis formosa was recorded for the first time on the shelf of the South Orkney Islands, which is the southernmost record of this species. New material and literature data demonstrate the existence of two discontinuous lithodid faunas: the Antarctic Pacific fauna that extends up to the western Antarctic Peninsula and the Magellanic—Scotia fauna. The origin of this faunal discontinuity is discussed. The molecular barcodes (subunitI of the mitochondrial cytochrome-oxidase gene—COI) data for N. diomedeae and L. turkayi are provided for the first time. COI gene tree suggests that two main Subantarctic/Antarctic lineages of Lithodes, i.e. a pair Lithodes santolla/L. confundens and L. turkayi (with possibly closely related Lithodes murrayi and L. macquariae) are phylogenetically distant from each other as well as with low-latitude Pacific and Atlantic species of this genus.

Added: Oct 14, 2014
Article
Klein M., Clauss G., Slunyaev A. Physics of Fluids. 2017. Vol. 29. P. 047103-1-047103-17.

The investigation of dynamics of intense solitary wave groups of collinear surface waves is performed by means of numerical simulations of the Euler equations and laboratory experiments. The processes of solitary wave generation, reflection from a wall and collisions are considered. Steep solitary wave groups with characteristic steepness up to kAcr ~ 0.3 (where k is the dominant wavenumber, and Acr is the crest amplitude) are concerned. They approximately restore the structure after the interactions. In the course of the interaction with the wall and collisions the maximum amplitude of the wave crests is shown to enhance up to 2.5 times. A standing-wave-like structure occurs in the vicinity of the wall, with certain locations of nodes and antinodes regardless the particular phase of the reflecting wave group. A strong asymmetry of the maximal wave groups due to an anomalous set-up is shown in situations of collisions of solitons with different frequencies of the carrier. In some situations of head-on collisions the amplitude of the highest wave is larger than in overtaking collisions of the same solitons. The discovered effects in interactions of intense wave groups are important in the context of mechanisms and manifestations of oceanic rogue waves.

Added: Feb 14, 2019
Article
Abrashkin A. A., Pelinovsky E. Nonlinear Processes in Geophysics. 2017. Vol. 24. P. 255-264.

The nonlinear Schrödinger (NLS) equation describing the propagation of weakly rotational wave packets in an infinitely deep fluid in Lagrangian coordinates has been derived. The vorticity is assumed to be an arbitrary function of Lagrangian coordinates and quadratic in the small parameter proportional to the wave steepness. The vorticity effects manifest themselves in a shift of the wave number in the carrier wave and in variation in the coefficient multiplying the nonlinear term. In the case of vorticity dependence on the vertical Lagrangian coordinate only (Gouyon waves), the shift of the wave number and the respective coefficient are constant. When the vorticity is dependent on both Lagrangian coordinates, the shift of the wave number is horizontally inhomogeneous. There are special cases (e.g., Gerstner waves) in which the vorticity is proportional to the squared wave amplitude and nonlinearity disappears, thus making the equations for wave packet dynamics linear. It is shown that the NLS solution for weakly rotational waves in the Eulerian variables may be obtained from the Lagrangian solution by simply changing the horizontal coordinates.

Added: Jun 26, 2017
Article
Dagaev N., Volkova K., Ossadtchi A. Journal of Neural Engineering. 2018. Vol. 15. No. 1. P. 1-14.

Objective. Brain-computer interface (BCI) systems are known to be vulnerable to variabilities in background states of a user. Usually, no detailed information on these states is available even during the training stage. Thus there is a need in a method which is capable of taking background states into account in an unsupervised way. Approach. We propose a latent variable method that is based on a probabilistic model with a discrete latent variable. In order to estimate the model's parameters, we suggest to use the expectation maximization (EM) algorithm. The proposed method is aimed at assessing characteristics of background states without any corresponding data labeling. In the context of asynchronous motor imagery paradigm, we applied this method to the real data from twelve able-bodied subjects with open/closed eyes serving as background states. Main results. We found that the latent variable method improved classication of target states compared to the baseline method (in seven of twelve subjects). In addition, we found that our method was also capable of background states recognition (in six of twelve subjects). Signicance. Without any supervised information on background states, the latent variable method provides a way to improve classication in BCI by taking background states into account at the training stage and then by making decisions on target states weighted by posterior probabilities of background states at the prediction stage.

Added: Oct 19, 2017
Article
Kokorina A., Slunyaev A. Fluids, Switzerland. 2019. Vol. 4. P. 70-1-70-16.

The issue of rogue wave lifetimes is addressed in this study, which helps to detail the general picture of this dangerous oceanic phenomenon. The direct numerical simulations of irregular wave ensembles are performed to obtain the complete accurate data on the rogue wave occurrence and evolution. Purely collinear wave systems, moderately crested, and short-crested sea states have been simulated by means of the high-order spectral method for the potential Euler equations. As rogue waves are transient and poorly reflect the physical e ects, we join instant abnormally high waves in close locations and close time moments to new objects, rogue events, which helps to retrieve the abnormal occurrences more stably and more consistently from the physical point of view. The rogue event lifetime probability distributions are calculated based on the simulated wave data. They show the distinctive di erence between rough sea states with small directional bandwidth on one part, and small-amplitude sea states and short-crested states on the other part. The former support long-living rogue wave patterns (the corresponding probability distributions have heavy tails), though the latter possess exponential probability distributions of rogue event lifetimes and generally produce much shorter rogue wave events.

Added: Apr 17, 2019
Article
Chugunov A. O., Pyrkova D. V., Nolde D. E. et al. Scientific Reports. 2013. Vol. 3. No. 1678.

Bacterial cell wall is targeted by many antibiotics. Among them are lantibiotics, which realize their function via interaction with transmembrane lipid-II molecule — a chemically conserved part of the cell wall synthesis pathway. To investigate structural and dynamic properties of this molecule, we have performed a series of nearly microsecond-long molecular dynamics simulations (MD) of lipid-II and some of its analogs in zwitterionic single component and charged mixed model phospholipid bilayers (the reference and mimic of the bacterial plasmatic membrane, respectively). Extensive analysis revealed that lipid-II forms a unique “amphiphilic pattern” exclusively on the surface of the model bacterial membrane (and not in the reference bilayer). We hypothesize that conserved features of lipid-II along with characteristic modulation of the bacterial membrane provide a recognition spot for many lantibiotics. This putative recognition mechanism opens new opportunities for studies on lantibiotics action and design of novel armament against resistant bacterial strains.

Added: Nov 13, 2013
Article
Hohlefeld F. U., Huebl J., Huchzermeyer C. et al. European Journal of Neuroscience. 2012. Vol. 6. No. 36. P. 2812-2821.

Neuronal activity in the subthalamic nucleus (STN) of patients with Parkinson's disease (PD) is characterised by excessive neuronal synchronization, particularly in the beta frequency range. However, less is known about the temporal dynamics of neuronal oscillations in PD. In this respect long-range temporal correlations (LRTC) are of special interest as they quantify the neuronal dynamics on different timescales and have been shown to be relevant for optimal information processing in the brain. While the presence of LRTC has been demonstrated in cortical data, their existence in deep brain structures remains an open question. We investigated (i) whether LRTC are present in local field potentials (LFP) recorded bilaterally from the STN at wakeful rest in ten patients with PD after overnight withdrawal of levodopa (OFF) and (ii) whether LRTC can be modulated by levodopa treatment (ON). Detrended fluctuation analysis was utilised in order to quantify the temporal dynamics in the amplitude fluctuations of LFP oscillations. We demonstrated for the first time the presence of LRTC (extending up to 50 s) in the STN. Importantly, the ON state was characterised by significantly stronger LRTC than the OFF state, both in beta (13-35 Hz) and high-frequency (> 200 Hz) oscillations. The existence of LRTC in subcortical structures such as STN provides further evidence for their ubiquitous nature in the brain. The weaker LRTC in the OFF state might indicate limited information processing in the dopamine-depleted basal ganglia. The present results implicate LRTC as a potential biomarker of pathological neuronal processes in PD.

Added: Oct 23, 2014
Article
Pelinovsky E., Rybkin A., Nikolsky D. et al. JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS. 2018. Vol. 123. No. 3. P. 2066-2080.

Modeling of tsunamis in glacial fjords prompts us to evaluate applicability of the crosssectionally averaged nonlinear shallow water equations to model propagation and runup of long waves in asymmetrical bays and also in fjords with two heads. We utilize the Tuck-Hwang transformation, initially introduced for the plane beaches and currently generalized for bays with arbitrary cross section, to transform the nonlinear governing equations into a linear equation. The solution of the linearized equation describing the runup at the shore line is computed by taking into account the incident wave at the toe of the last sloping segment. We verify our predictions against direct numerical simulation of the 2-D shallow water equations and show that our solution is valid both for bays with an asymmetric L-shaped cross section, and for fjords with two heads—bays with a W-shaped cross section

Added: Oct 21, 2018
Article
Пелиновский Е. Н., Didenkulova I., Rodin A. Известия РАН. Механика жидкости и газа. 2018. Т. 53. № 3. С. 402-408.

The long wave run-up on two types of slopes is investigated numerically within the framework of nonlinear shallow water theory using the CLAWPACK software. One of the slopes represents a plane slope widely used in the laboratory and numerical experiments; the second is the so-called “non-reflecting” slope (h ∼ x4/3, where h is the basin depth and x is the distance from the shoreline). In the case of very low wave amplitudes when there is no wave breaking, the run-up height is greater on the non-reflecting beach than that on the plane slope. As the wave amplitude increases, the breaking effects have the stronger impact in the case of non-reflecting beach and the run-up height becomes smaller.

Added: Oct 21, 2018
Article
Moseley R., Shtyrov Yury, Mohr B. et al. Neuroimage. 2015. Vol. 104. P. 413-422.

Autism spectrum conditions (ASC) are characterised by deficits in understanding and expressing emotions and are frequently accompanied by alexithymia, a difficulty in understanding and expressing emotion words. Words are differentially represented in the brain according to their semantic category and these difficulties in ASC predict reduced activation to emotion-related words in limbic structures crucial for affective processing. Semantic theories view 'emotion actions' as critical for learning the semantic relationship between a word and the emotion it describes, such that emotion words typically activate the cortical motor systems involved in expressing emotion actions such as facial expressions. As ASC are also characterised by motor deficits and atypical brain structure and function in these regions, motor structures would also be expected to show reduced activation during emotion-semantic processing. Here we used event-related fMRI to compare passive processing of emotion words in comparison to abstract verbs and animal names in typically-developing controls and individuals with ASC. Relatively reduced brain activation in ASC for emotion words, but not matched control words, was found in motor areas and cingulate cortex specifically. The degree of activation evoked by emotion words in the motor system was also associated with the extent of autistic traits as revealed by the Autism Spectrum Quotient. We suggest that hypoactivation of motor and limbic regions for emotion-word processing may underlie difficulties in processing emotional language in ASC. The role that sensorimotor systems and their connections might play in the affective and social-communication difficulties in ASC is discussed.

Added: Oct 23, 2014
Article
O. Kurkina, T. Talipova, E. Pelinovsky et al. Journal of Coastal Research. 2011. No. SI64. P. 2042-2047.

The geographical and seasonal distributions of kinematic and nonlinear parametersof long internal waves obtained on a base of GDEM climatology in the Baltic Sea region are examined. The considered parameters (phase speed of long internal wave, dispersion, quadratic and cubicnonlinearity parameters) of the weakly-nonlinear Korteweg-de Vries-type models (in particular, Gardner model), can be used for evaluations of the possible polarities, shapes of solitary internal waves, their limiting amplitudes and propagation speeds. The key outcome is an express estimate of the expected internal wave parameters for different regions of the Baltic Sea. The central kinematic characteristic is the near-bottom velocity in internal waves in areas where the density jump layers are located in the vicinity of seabed. In such areas internal waves are the major driver of sediment resuspension and erosion processes and may be also responsible for destroying the laminated structure of sedimentation regime (that frequently occurs in certain areas of the Baltic Sea).

Added: Oct 11, 2012
Article
Tikunov V., Riazantsev S., Timonin S. Annals of GIS. 2013. Vol. 19. No. 1. P. 17-25.

This article is devoted to the study of the population’s ethnic structure in regions of Russia and former RSFSR (Russian Soviet Federative Socialist Republic) as well as the temporal dynamics of major ethnic groups by means of mathematical and cartographic modelling. Integrated indicators are developed to estimate ethnic diversity in regions of Russia and former RSFSR (ethnic diversity index and its modification – ethnic diversity index adjusted for the ability to speak Russian), and cluster analysis is performed to offer typological classification of Russian regions based on their ethnic composition. Maps are created on the basis of the derived indicators and typological classification. Finally, the estimates of the share of major ethnic groups up to 2030 are provided.

Added: Mar 12, 2013
Article
Logvenkov S. A., Moiseeva I., Stein A. Biofizika. 2016. Vol. 61. No. 6. P. 989-995.

Invagination of epithelial sheets is an important type of morphogenetic deformation. Primary invagination during gastrulation in the sea urchin provides one of the simplest and best-studied examples. The specific mechanisms of invagination remain unclear in spite of numerous observations. The problem of plane-stress deformation of an initially circular layer exposed to a constant internal pressure is considered. Active forces developed by cells are characterized by an active moment. The rheology of a layer is described by a Maxwell-type viscoelasticity equation, which links the passive bending moment with the curvature of the layer. The presence of a passive moment threshold below which bending is purely elastic is taken into account. The active moment is defined as a function of coordinates and time that is nonzero in a certain limited region. The function is assumed to gradually increase, reach a steady state, and then decline gradually. Both constant- and alternating-sign spatial distributions of the active moment are considered. Numerical simulation showed that among all of the considered variants a realistic sequence of shapes can only be obtained if the layer is viscoelastic, there is a finite threshold for the passive bending moment, and the distribution of the active moment is of an alternating-sign type. The sign of the active moment differs between the inner and outer areas of the active region, tending to bend the sheet inward in the inner area and outward in the outer area. This study made it possible to reach several conclusions on the nature of the macroscopic organization of invagination and to outline avenues of research into the cellular mechanisms that are capable of developing the corresponding forces.

Added: Feb 14, 2017
Article
Logvenkov S. A., Stein A. Biofizika. 2015. Vol. 60. No. 6. P. 977-982.

The problem of deformation of a planar embryonic epithelium layer that is unloaded after a short period of uniaxial stretching with subsequent fixation in the stretched state for different periods of time is solved. The initial conditions for solving this problem are derived from the previously discussed problem of the uniform stretching of a tissue fragment (explant) with subsequent fixation of the obtained length. In this study we used the previously developed continuum model that describes the stress–strain state of epithelial tissue taking the parameters that characterize the shape of the cells and their stress state into account, as well as the active stresses they exert when they interact with each other. The experimentally observed continuation of the deformation of a stretched tissue after the external force has ceased to act is described theoretically as a result of active cell reactions to mechanical stress. The duration of explant fixation is shown to have a strong effect on its further elongation and on the pattern of cell activity.

Added: Feb 5, 2016
Article
Beloussov L., Logvenkov S. A., Stein A. Fluid Dynamics. 2015. Vol. 50. No. 1. P. 1-11.

A continuum model of the embryonic epithelial tissue with account for the active deformations and rearrangements of the cells is proposed. The stress tensor is represented as the sum of the stresses undergone by the cell directly and the tensor of active stresses that arise owing to contracting cellular protrusions anchored on the surface of neighboring cells and developing in response to cell reshaping (deformation). The strain rate tensor includes three components: elastic and two inelastic related to the active deformation of the cells and their rearrangement. The first of these components depends on the stresses in the cells and the reached cellular deformation level, whereas the second is determined by the active stresses. The problem of reaction of a thin sheet to a rapid stretching is solved and agreement with experimental data is obtained.

Added: Jan 25, 2015