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Regular version of the site
Of all publications in the section: 53
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Article
Yakubova A., Thorrez L., Svetlichnyy D. et al. Scientific Reports. 2018. Vol. 8. No. 1. P. 1-12.

Cardiovascular disease associated with metabolic syndrome has a high prevalence, but the mechanistic basis of metabolic cardiomyopathy remains poorly understood. We characterised the cardiac transcriptome in a murine metabolic syndrome (MetS) model (LDLR−/−; ob/ob, DKO) relative to the healthy, control heart (C57BL/6, WT) and the transcriptional changes induced by ACE-inhibition in those hearts. RNA-Seq, differential gene expression and transcription factor analysis identified 288 genes differentially expressed between DKO and WT hearts implicating 72 pathways. Hallmarks of metabolic cardiomyopathy were increased activity in integrin-linked kinase signalling, Rho signalling, dendritic cell maturation, production of nitric oxide and reactive oxygen species in macrophages, atherosclerosis, LXR-RXR signalling, cardiac hypertrophy, and acute phase response pathways. ACE-inhibition had a limited effect on gene expression in WT (55 genes, 23 pathways), and a prominent effect in DKO hearts (1143 genes, 104 pathways). In DKO hearts, ACE-I appears to counteract some of the MetS-specific pathways, while also activating cardioprotective mechanisms. We conclude that MetS and control murine hearts have unique transcriptional profiles and exhibit a partially specific transcriptional response to ACE-inhibition.

Added: Nov 2, 2018
Article
Tarkhov A., Alla R., Ayyadevara S. et al. Scientific Reports. 2019. Vol. 9. No. 1. P. 1-18.

We collected 60 age-dependent transcriptomes for C. elegans strains including four exceptionally long-lived mutants (mean adult lifespan extended 2.2- to 9.4-fold) and three examples of lifespan-increasing RNAi treatments. Principal Component Analysis (PCA) reveals aging as a transcriptomic drift along a single direction, consistent across the vastly diverse biological conditions and coinciding with the first principal component, a hallmark of the criticality of the underlying gene regulatory network. We therefore expected that the organism's aging state could be characterized by a single number closely related to vitality deficit or biological age. The "aging trajectory", i.e. the dependence of the biological age on chronological age, is then a universal stochastic function modulated by the network stiffness; a macroscopic parameter reflecting the network topology and associated with the rate of aging. To corroborate this view, we used publicly available datasets to define a transcriptomic biomarker of age and observed that the rescaling of age by lifespan simultaneously brings together aging trajectories of transcription and survival curves. In accordance with the theoretical prediction, the limiting mortality value at the plateau agrees closely with the mortality rate doubling exponent estimated at the cross-over age near the average lifespan. Finally, we used the transcriptomic signature of age to identify possible life-extending drug compounds and successfully tested a handful of the top-ranking molecules in C. elegans survival assays and achieved up to a +30% extension of mean lifespan.

Added: Oct 7, 2019
Article
K. I. Kugel, Oveshnikov L. N., Kulbachinskii V. A. et al. Scientific Reports. 2015. Vol. 5. P. 17158-1-17158-9.
The anomalous Hall effect (AHE) arises from the interplay of spin-orbit interactions and ferromagnetic order and is a potentially useful probe of electron spin polarization, especially in nanoscale systems where direct measurement is not feasible. While AHE is rather well-understood in metallic ferromagnets, much less is known about the relevance of different physical mechanisms  governing AHE in insulators. As ferromagnetic insulators, but not metals, lend themselves to gate control of electron spin olarization, understanding AHE in the insulating state is valuable from the point of view of spintronic applications. Among the mechanisms proposed in the literature for AHE in insulators, the one related to a geometric (Berry) phase effect has been elusive in past studies.The recent discovery of quantized AHE in magnetically doped topological insulators - essentially a Berry phase effect - provides strong additional motivation to undertake more careful search for geometric phase effects in AHE in the magnetic semiconductors. Here we report our experiments on the temperature and magnetic field dependences of AHE in insulating, strongly-disordered two-dimensional Mn delta-doped semiconductor heterostructures in the hopping regime. In particular, it is shown that at sufficiently low temperatures, the mechanism of AHE related to the Berry phase is favoured.
Added: Mar 13, 2016
Article
Zinchenko O. O. Scientific Reports. 2019. Vol. 9. No. 12800. P. 1-8.

Many studies suggest that social punishment is beneficial for cooperation and consequently maintaining the social norms in society. Neuroimaging and brain stimulation studies show that the brain regions which respond to violations of social norms, the understanding of the mind of others and the executive functions, are involved during social punishment. Despite the rising number of studies on social punishment, the concordant map of activations - the set of key regions responsible for the general brain response to social punishment - is still unknown. By using coordinate-based fMRI meta-analysis, the present study examined the concordant map of neural activations associated with various social punishment tasks. A total of 17 articles with 18 contrasts including 383 participants, equalling 191 foci were included in activation likelihood estimation (ALE) analysis. The majority of the studies (61%) employed the widely used neuroeconomic paradigms, such as fairness-related norm tasks (Ultimatum Game, third-party punishment game), while the remaining tasks reported included criminal scenarios evaluation and social rejection tasks. The analysis presented revealed concordant activation in the bilateral claustrum, right interior frontal and left superior frontal gyri. This study provides an integrative view on brain responses to social punishment.

Added: Sep 6, 2019
Article
Mesitov M., Soldatov R., Zaichenko D. et al. Scientific Reports. 2017. Vol. 7. P. 1-14.

The accumulation of misfolded proteins in the endoplasmic reticulum (ER) lumen due to the disruption of the homeostatic system of the ER leads to the induction of the ER stress response. Cellular stress-induced pathways globally transform genes expression on both the transcriptional and post-transcriptional levels with small RNA involvement as regulators of the stress response. The modulation of small RNAprocessing might represent an additional layer of a complex stress response program. However, it is poorly understood. Here, we studied changes in expression and small RNAs processing upon ER stress in Jurkat T-cells. Induced by ER-stress, depletion of miRNAs among small RNA composition was accompanied by a global decrease of 3' mono-adenylated, mono-cytodinylated and a global increase of 3' mono-uridinylated miRNA isoforms. We observed the specific subset of differentially expressed microRNAs, and also the dramatic induction of 32-nt tRNA fragments precisely phased to 5' and 3' ends of tRNA from a subset of tRNA isotypes. The induction of these tRNA fragments was linked to Angiogenin RNase, which mediates translation inhibition. Overall, the global perturbations of the expression and processing of miRNAs and tiRNAs were the most prominent features of small RNA transcriptome changes upon ER stress.

Added: Mar 14, 2018
Article
Demishev S. V., Krasnorussky V. N., Bogach A. V. et al. Scientific Reports. 2017. Vol. 7. P. 17430-1-17430-8.

Spatial anisotropy generated spontaneously in the translationally invariant metallic phase, i.e. electron nematic efect, addresses a great challenge for both experimentalists and theoreticians. An interesting option for the realization of the electron nematic phase is provided by the system with orbital ordering, as long as both orbitally ordered states and electron nematic phases possess broken spatial symmetry. Here we report the detailed study of the angular dependences of the magnetoresistance in the orbitally ordered antiferroquadrupole (AFQ) phase of CeB6. Our data allowed revealing the electron nematic efect, which develops when magnetic feld exceeds a critical value of 0.3–0.5T. As a result, new transition inside the AFQ phase corresponding to the change of the symmetry of magnetic scattering on spin fuctuations in CeB6 is discovered.

Added: Mar 10, 2018
Article
Averyanov D. V., Tokmachev A. M., Karateeva K. G. et al. Scientific Reports. 2016. No. 6.

Metal-silicon junctions are crucial to the operation of semiconductor devices: aggressive scaling demands low-resistive metallic terminals to replace high-doped silicon in transistors. It suggests an efficient charge injection through a low Schottky barrier between a metal and Si. Tremendous efforts invested into engineering metal-silicon junctions reveal the major role of chemical bonding at the interface: premier contacts entail epitaxial integration of metal silicides with Si. Here we present epitaxially grown EuSi2/Si junction characterized by RHEED, XRD, transmission electron microscopy, magnetization and transport measurements. Structural perfection leads to superb conductivity and a record-low Schottky barrier with n-Si while an antiferromagnetic phase invites spin-related applications. This development opens brand-new opportunities in electronics.

Added: Jun 2, 2016
Article
Pyrkov T., Slipensky K., Barg M. et al. Scientific Reports. 2018. Vol. 8. No. 1. P. 1-11.

Age-related physiological changes in humans are linearly associated with age. Naturally, linear combinations of physiological measures trained to estimate chronological age have recently emerged as a practical way to quantify aging in the form of biological age. In this work, we used oneweek long physical activity records from a 2003–2006 National Health and Nutrition Examination Survey (NHANES) to compare three increasingly accurate biological age models: the unsupervised Principal Components Analysis (PCA) score, a multivariate linear regression, and a state-of-theart deep convolutional neural network (CNN). We found that the supervised approaches produce better chronological age estimations at the expense of a loss of the association between the aging acceleration and all-cause mortality. Consequently, we turned to the NHANES death register directly and introduced a novel way to train parametric proportional hazards models suitable for out-of-thebox implementation with any modern machine learning software. As a demonstration, we produced a separate deep CNN for mortality risks prediction that outperformed any of the biological age or a simple linear proportional hazards model. Altogether, our findings demonstrate the emerging potential of combined wearable sensors and deep learning technologies for applications involving continuous health risk monitoring and real-time feedback to patients and care providers.

Added: Oct 29, 2018
Article
Savochkin I. V., Jäckl M., Belotelov V. I. et al. Scientific Reports. 2017. No. 5668. P. 1-10.

Currently spin waves are considered for computation and data processing as an alternative to charge currents. Generation of spin waves by ultrashort laser pulses provides several important advances with respect to conventional approaches using microwaves. In particular, focused laser spot works as a point source for spin waves and allows for directional control of spin waves and switching between their different types. For further progress in this direction it is important to manipulate with the spectrum of the optically generated spin waves. Here we tackle this problem by launching spin waves by a sequence of femtosecond laser pulses with pulse interval much shorter than the relaxation time of the magnetization oscillations. This leads to the cumulative phenomenon and allows us to generate magnons in a specific narrow range of wavenumbers. The wavelength of spin waves can be tuned from 15μm to hundreds of microns by sweeping the external magnetic field by only 10Oe or by slight variation of the pulse repetition rate. Our findings expand the capabilities of the optical spin pumpprobe technique and provide a new method for the spin wave generation and control.

Added: Feb 27, 2018
Article
Flegontov P., et a., Gelfand M. S. et al. Scientific Reports. 2016. Vol. 6. P. 1-12.

The Kets, an ethnic group in the Yenisei River basin, Russia, are considered the last nomadic hunter-gatherers of Siberia, and Ket language has no transparent affiliation with any language family. We investigated connections between the Kets and Siberian and North American populations, with emphasis on the Mal'ta and Paleo-Eskimo ancient genomes, using original data from 46 unrelated samples of Kets and 42 samples of their neighboring ethnic groups (Uralic-speaking Nganasans, Enets, and Selkups). We genotyped over 130,000 autosomal SNPs, identified mitochondrial and Y-chromosomal haplogroups, and performed high-coverage genome sequencing of two Ket individuals. We established that Nganasans, Kets, Selkups, and Yukaghirs form a cluster of populations most closely related to Paleo-Eskimos in Siberia (not considering indigenous populations of Chukotka and Kamchatka). Kets are closely related to modern Selkups and to some Bronze and Iron Age populations of the Altai region, with all these groups sharing a high degree of Mal'ta ancestry. Implications of these findings for the linguistic hypothesis uniting Ket and Na-Dene languages into a language macrofamily are discussed.

Added: Mar 13, 2017
Article
Volodina M., Vishnyakova P., Tarasova N. et al. Scientific Reports. 2019. Vol. 9. No. 1. P. 1-11.

Calcium plays a role of universal cellular regulator in the living cell and one of the crucial regulators of proper fetal development during gestation. Mitochondria are important for intracellular calcium handling and signaling. Mitochondrial calcium uniporter (mtCU) is a multiprotein complex of the mitochondrial inner membrane responsible for the transport of calcium to the mitochondrial matrix. In the present study, we analyzed the expression level of mtCU components in two parts of the feto-maternal system - placenta and myometrium at full-term delivery and at preterm birth (PTB) on different stages: 22-27, 28-32, 33-36 weeks of gestation (n = 50). A gradual increase of mRNA expression and changes in protein content of MCU and MICU1 subunits were revealed in the placenta during gestation. We also observed slower depolarization rate of isolated placental mitochondria induced by Ca2+ titration at PTB. In myometrium at PTB relative gene expression level of MCU, MCUb and SMDT1 increased as compared to full-term pregnancy, but the tendency to gradual increase of MCU protein simultaneous with MCUb increase and MICU1 decline was shown in gestational dynamics. Changes observed in the present study might be considered both natural dynamics as well as possible pathological mechanisms underlying preterm birth.

Added: May 15, 2019
Article
Kasheverov I., Chugunov A., Kudryavtsev D. et al. Scientific Reports. 2016. Vol. 6. No. 36848. P. 1-11.

Despite some success for small molecules, elucidating structure–function relationships for biologically active peptides — the ligands for various targets in the organism — remains a great challenge and calls for the development of novel approaches. Some of us recently proposed the Protein Surface Topography (PST) approach, which benefits from a simplified representation of biomolecules’ surface as projection maps, which enables the exposure of the structure–function dependencies. Here, we use PST to uncover the “activity pattern” in α-conotoxins — neuroactive peptides that effectively target nicotinic acetylcholine receptors (nAChRs). PST was applied in order to design several variants of the α-conotoxin PnIA, which were synthesized and thoroughly studied. Among the best was PnIA[R9, L10], which exhibits nanomolar affinity for the α7 nAChR, selectivity and a slow wash-out from this target. Importantly, these mutations could hardly be delineated by “standard” structure-based drug design. The proposed combination of PST with a set of experiments proved very efficient for the rational construction of new bioactive molecules.

Added: Mar 14, 2017
Article
V. V. Galatenko, Shkurnikov M. Y., Samatov T. R. et al. Scientific Reports. 2015. Vol. 5.

Genes with significant differential expression are traditionally used to reveal the genetic background underlying phenotypic differences between cancer cells. We hypothesized that informative marker sets can be obtained by combining genes with a relatively low degree of individual differential expression. We developed a method for construction of highly informative gene combinations aimed at the maximization of the cumulative informative power and identified sets of 2–5 genes efficiently predicting recurrence for ER-positive breast cancer patients. The gene combinations constructed on the basis of microarray data were successfully applied to data acquired by RNA-seq. The developed method provides the basis for the generation of highly efficient prognostic and predictive gene signatures for cancer and other diseases. The identified gene sets can potentially reveal novel essential segments of gene interaction networks and pathways implied in cancer progression.

Added: Oct 27, 2015
Article
Kimppa L., Kujala T., Shtyrov Y. Scientific Reports. 2016. No. 6. P. 30227.

Mastering multiple languages is an increasingly important ability in the modern world; furthermore, multilingualism may affect human learning abilities. Here, we test how the brain’s capacity to rapidly form new representations for spoken words is affected by prior individual experience in non-native language acquisition. Formation of new word memory traces is reflected in a neurophysiological response increase during a short exposure to novel lexicon. Therefore, we recorded changes in electrophysiological responses to phonologically native and non-native novel word-forms during a perceptual learning session, in which novel stimuli were repetitively presented to healthy adults in either ignore or attend conditions. We found that larger number of previously acquired languages and earlier average age of acquisition (AoA) predicted greater response increase to novel non-native word-forms. This suggests that early and extensive language experience is associated with greater neural flexibility for acquiring novel words with unfamiliar phonology. Conversely, later AoA was associated with a stronger response increase for phonologically native novel word-forms, indicating better tuning of neural linguistic circuits to native phonology. The results suggest that individual language experience has a strong effect on the neural mechanisms of word learning, and that it interacts with the phonological familiarity of the novel lexicon.

Added: Sep 8, 2016
Article
Lebedev M., Tseng P., Rajangam S. et al. Scientific Reports. 2018. Vol. 8. No. 4699. P. 1-15.

While it is well known that the primate brain evolved to cope with complex social contingencies, the neurophysiological manifestation of social interactions in primates is not well understood. Here, concurrent wireless neuronal ensemble recordings from pairs of monkeys were conducted to measure interbrain cortical synchronization (ICS) during a whole-body navigation task that involved continuous social interaction of two monkeys. One monkey, the passenger, was carried in a robotic wheelchair to a food dispenser, while a second monkey, the observer, remained stationary, watching the passenger. The two monkeys alternated the passenger and the observer roles. Concurrent neuronal ensemble recordings from the monkeys' motor cortex and the premotor dorsal area revealed episodic occurrence of ICS with probability that depended on the wheelchair kinematics, the passenger-observer distance, and the passenger-food distance - the social-interaction factors previously described in behavioral studies. These results suggest that ICS represents specific aspectsof primate social interactions.

Added: Dec 11, 2018
Article
Dolgirev P., Kalenkov M., Zaikin Andrei D. Scientific Reports. 2019. Vol. 9. P. 1-9.

Proximity induced quantum coherence of electrons in multi-terminal voltage-driven hybrid normalsuperconducting nanostructures may result in a non-trivial interplay between topology-dependent Josephson and Aharonov-Bohm effects. We elucidate a trade-off between stimulation of the voltagedependent Josephson current due to non-equilibrium effects and quantum dephasing of quasiparticles causing reduction of both Josephson and Aharonov-Bohm currents. We also predict phase-shifted quantum coherent oscillations of the induced electrostatic potential as a function of the externally applied magnetic flux. Our results may be employed for engineering superconducting nanocircuits with controlled quantum properties.

Added: Mar 11, 2019
Article
Backens S., Shnirman A., Makhlin Y. Scientific Reports. 2019. Vol. 9. P. 1-8.

The celebrated Jordan–Wigner transformation provides an efficient mapping between spin chains and fermionic systems in one dimension. Here we extend this spin–fermion mapping to arbitrary tree structures, which enables mapping between fermionic and spin systems with nearest-neighbor coupling. The mapping is achieved with the help of additional spins at the junctions between one-dimensional chains. This property allows for straightforward simulation of Majorana braiding in spin or qubit systems.

Added: Feb 24, 2019
Article
Kornilov S. A., Zhukova M. A., Ovchinnikova I. V. et al. Scientific Reports. 2019. Vol. 9. P. 1-13.

Impoverished early care environments are associated with developmental deficits in children raised in institutional settings. Despite the accumulation of evidence regarding deficits in general cognitive functioning in this population, less is known about the impact of institutionalization on language development at the level of brain and behavior. We examined language outcomes in young adults and adolescents raised in institutions (n = 23) as compared to their socioeconomic status and age peers raised in biological families (n = 24) using a behavioral language assessment and linguistic event-related potentials (ERPs). Controlling for intelligence, adults with a history of institutionalization demonstrated deficits in lexical and grammatical development and spelling. Analyses of ERP data revealed significant group differences in the dynamic processing of linguistic stimuli. Adults with a history of institutionalization displayed reduced neural sensitivity to violations of word expectancy, leading to reduced condition effects for temporo-spatial factors that tentatively corresponded to the N200, P300/N400, and phonological mismatch negativity. The results suggest that language is a vulnerable domain in adults with a history of institutionalization, the deficits in which are not explained by general developmental delays, and point to the pivotal role of early linguistic environment in the development of the neural networks involved in language processing.

Added: Mar 13, 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
Chugunov A., Volynsky P., Krylov N. et al. Scientific Reports. 2014. Vol. 4. No. 7462. P. 1-8.

Archaeal plasma membranes appear to be extremely durable and almost impermeable to water and ions, in contrast to the membranes of Bacteria and Eucaryota. Additionally, they remain liquid within a temperature range of 0–100° С. These are the properties that have most likely determined the evolutionary fate of Archaea, and it may be possible for bionanotechnology to adopt these from nature. In this work, we use molecular dynamics simulations to assess at the atomic level the structure and dynamics of a series of model archaeal membranes with lipids that have tetraether chemical nature and “branched” hydrophobic tails. We conclude that the branched structure defines dense packing and low water permeability of archaeal-like membranes, while at the same time ensuring a liquid-crystalline state, which is vital for living cells. This makes tetraether lipid systems promising in bionanotechnology and material science, namely for design of new and unique membrane nanoobjects.

Added: Jul 21, 2015
Article
Tikhonov E., Shovkun D. V., Ercolani D. et al. Scientific Reports. 2016. Vol. 6. No. 30621. P. 1-7.

The control and measurement of local non-equilibrium configurations is of utmost importance in applications on energy harvesting, thermoelectrics and heat management in nano-electronics. This challenging task can be achieved with the help of various local probes, prominent examples including superconducting or quantum dot based tunnel junctions, classical and quantum resistors, and Raman thermography. Beyond time-averaged properties, valuable information can also be gained from spontaneous fluctuations of current (noise). From these perspective, however, a fundamental constraint is set by current conservation, which makes noise a characteristic of the whole conductor, rather than some part of it. Here we demonstrate how to remove this obstacle and pick up a local noise temperature of a current biased diffusive conductor with the help of a miniature noise probe. This approach is virtually noninvasive for the electronic energy distributions and extends primary local measurements towards strongly non-equilibrium regimes.

Added: Feb 1, 2019