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Of all publications in the section: 106
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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
Iakobson O. D., Gribkova O. L., Aleksey Tameev et al. Scientific Reports. 2021. Vol. 11. P. 5005-1-5005-6.

The structure of experimentally designed solar cells was optimized in terms of the photoactive layer thickness for both organic bulk heterojunction and hybrid perovskite solar cells. The photoactive layer thickness had a totally different behavior on the performance of the organic and hybrid solar cells. Analysis of the optical parameters using transfer matrix modeling within the Maxwell–Garnett effective refractive index model shows that light absorbance and exciton generation rate in the photoactive layer can be used to optimize the thickness range of the photoactive layer. Complete agreement between experimental and simulated data for solar cells with photoactive materials that have very different natures proves the validity of the proposed modeling method. The proposed simple method which is not time-consuming to implement permits to obtain a preliminary assessment of the reasonable range of layer thickness that will be needed for designing experimental samples.

Added: Mar 4, 2021
Article
Min Namkung, Younghun K. Scientific Reports. 2019. Vol. 9. No. 1. P. 19664-1-19664-19.

Quantum state discrimination of coherent states has been one of important problems in quantum information processing. Recently, R. Han et al. showed that minimum error discrimination of two coherent states can be nearly done by using Jaynes-Cummings Hamiltonian. In this paper, based on the result of R. Han et al., we propose the methods where minimum error discrimination of more than two weak coherent states can be nearly performed. Specially, we construct models which can do almost minimum error discrimination of three and four coherent states. Our result can be applied to quantum information processing of various coherent states.

Added: Nov 16, 2020
Article
Lebedev M., Ossadtchi A., Urpí N. A. et al. Scientific Reports. 2019. Vol. 9. No. 1. P. 1-14.

Back in 2012, Churchland and his colleagues proposed that “rotational dynamics”, uncovered through linear transformations of multidimensional neuronal data, represent a fundamental type of neuronal population processing in a variety of organisms, from the isolated leech central nervous system to the primate motor cortex. Here, we evaluated this claim using Churchland’s own data and simple simulations of neuronal responses. We observed that rotational patterns occurred in neuronal populations when (1) there was a temporal sequence in peak firing rates exhibited by individual neurons, and (2) this sequence remained consistent across different experimental conditions. Provided that such a temporal order of peak firing rates existed, rotational patterns could be easily obtained using a rather arbitrary computer simulation of neural activity; modeling of any realistic properties of motor cortical responses was not needed. Additionally, arbitrary traces, such as Lissajous curves, could be easily obtained from Churchland’s data with multiple linear regression. While these observations suggest that temporal sequences of neuronal responses could be visualized as rotations with various methods, we express doubt about Churchland et al.’s bold assessment that such rotations are related to “an unexpected yet surprisingly simple structure in the population response”, which “explains many of the confusing features of individual neural responses”. Instead, we argue that their approach provides little, if any, insight on the underlying neuronal mechanisms employed by neuronal ensembles to encode motor behaviors in any species.

Added: Apr 14, 2020
Article
Min Namkung, Younghun K. Scientific Reports. 2018. Vol. 8. No. 1. P. 6515-1-6515-13.

Recently, J. A. Bergou et al. proposed sequential state discrimination as a new quantum state discrimination scheme. In the scheme, by the successful sequential discrimination of a qubit state, receivers Bob and Charlie can share the information of the qubit prepared by a sender Alice. A merit of the scheme is that a quantum channel is established between Bob and Charlie, but a classical communication is not allowed. In this report, we present a method for extending the original sequential state discrimination of two qubit states to a scheme of N linearly independent pure quantum states. Specifically, we obtain the conditions for the sequential state discrimination of N = 3 pure quantum states. We can analytically provide conditions when there is a special symmetry among N = 3 linearly independent pure quantum states. Additionally, we show that the scenario proposed in this study can be applied to quantum key distribution. Furthermore, we show that the sequential state discrimination of three qutrit states performs better than the strategy of probabilistic quantum cloning.

Added: Nov 16, 2020
Article
Galeeva A. V., Kazakov A. S., Artamkin A. I. et al. Scientific Reports. 2020. Vol. 10. P. 2377.

We show that the terahertz (THz) photoconductivity in the topological phase of Hg1–xCdxTe-based structures exhibits the apparent PT- (parity-time) symmetry whereas the P-symmetry and the T-symmetry, separately, are not conserved. Moreover, it is demonstrated that the P- and T-symmetry breaking may not be related to any type of the sample anisotropy. This result contradicts the apparent symmetry arguments and means that there exists an external factor that interacts with the sample electronic system and breaks the symmetry. We show that deviations from the ideal experimental geometry may not be such a factor.

Added: Mar 13, 2020
Article
Kachur A., Osin E. N., Davydov D. et al. Scientific Reports. 2020. Vol. 10. P. 8487.

There is ample evidence that morphological and social cues in a human face provide signals of human personality and behaviour. Previous studies have discovered associations between the features of artificial composite facial images and attributions of personality traits by human experts. We present new findings demonstrating the statistically significant prediction of a wider set of personality features (all the Big Five personality traits) for both men and women using real-life static facial images. Volunteer participants (N = 12,447) provided their face photographs (31,367 images) and completed a self-report measure of the Big Five traits. We trained a cascade of artificial neural networks (ANNs) on a large labelled dataset to predict self-reported Big Five scores. The highest correlations between observed and predicted personality scores were found for conscientiousness (0.360 for men and 0.335 for women) and the mean effect size was 0.243, exceeding the results obtained in prior studies using ‘selfies’. The findings strongly support the possibility of predicting multidimensional personality profiles from static facial images using ANNs trained on large labelled datasets. Future research could investigate the relative contribution of morphological features of the face and other characteristics of facial images to predicting personality.

Added: May 24, 2020
Article
Leal A., Rakov V. Scientific Reports. 2019. Vol. 9. P. 12218.

The occurrence context of compact intracloud discharges (CIDs) is examined using their electric field waveforms and corresponding NLDN data. A total of 1096 CIDs transporting negative charge upward and 8 CIDs transporting positive charge upward were analyzed. The CIDs were categorized based on whether they were isolated or were followed, preceded, or both followed and preceded by other NLDN-reported lightning events. The percentages of isolated CIDs transporting negative charge upward decreased from 92% for 5 km search radius and +/- 10 ms time window to 31% for 10 km and +/- 1000 ms, this decrease being accompanied by an increase of the percentage of CIDs preceding (initiating) normal lightning events from 6.8% to 43%. GM NLDN-reported peak currents for isolated CIDs (33 kA) were similar to those initiating normal lightning events (34 kA). Some of our isolated CIDs could be viewed as precursors, because they apparently initiated normal lightning events at essentially the same location after time intervals measured in seconds. CIDs transporting positive charge upward (a) occurred at heights ranging from 16 to 19 km vs. 6 to 16 km for CIDs transporting negative charge upward and (b) had considerably higher NLDN-reported peak currents: 113 kA vs. 33 kA (GM values).

Added: Nov 20, 2020
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. 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
Budylin Gleb S., Kudryavtsev D. S., Tabakmakher V. М. et al. Scientific Reports. 2020. Vol. 10. No. 3861. P. 1-13.

Snake venom α-neurotoxins, invaluable pharmacological tools, bind with high affinity to distinct subtypes of nicotinic acetylcholine receptor. The combinatorial high-affinity peptide (HAP), homologous to the C-loop of α1 and α7 nAChR subunits, binds biotinylated α-bungarotoxin (αBgt) with nanomolar affinity and might be a protection against snake-bites. Since there are no data on HAP interaction with other toxins, we checked its binding of α-cobratoxin (αCtx), similar to αBgt in action on nAChRs. Using radioiodinated αBgt, we confirmed a high affinity of HAP for αBgt, the complex formation is supported by mass spectrometry and gel chromatography, but only weak binding was registered with αCtx. A combination of protein intrinsic fluorescence measurements with the principal component analysis of the spectra allowed us to measure the HAP-αBgt binding constant directly (29 nM). These methods also confirmed weak HAP interaction with αCtx (>10000 nM). We attempted to enhance it by modification of HAP structure relying on the known structures of α-neurotoxins with various targets and applying molecular dynamics. A series of HAP analogues have been synthesized, HAP[L9E] analogue being considerably more potent than HAP in αCtx binding (7000 nM). The proposed combination of experimental and computational approaches appears promising for analysis of various peptide-protein interactions.

Added: May 14, 2020
Article
Galatenko Vladimir V., Galatenko Alexey V., Samatov T. R. et al. Scientific Reports. 2018. Vol. 8. P. 2418:1-2418:12.

MicroRNAs (miRNAs) are a family of short noncoding RNAs that posttranscriptionally regulate gene expression and play an important role in multiple cellular processes. A significant percentage of miRNAs are intragenic, which is often functionally related to their host genes playing either antagonistic or synergistic roles. In this study, we constructed and analyzed the entire network of intergenic interactions induced by intragenic miRNAs. We further focused on the core of this network, which was defined as a union of nontrivial strongly connected components, i.e., sets of nodes (genes) mutually connected via directed paths. Both the entire network and its core possessed statistically significant non-random properties. Specifically, genes forming the core had high expression levels and low expression variance. Furthermore, the network core did not split into separate components corresponding to individual signalling or metabolic pathways, but integrated genes involved in key cellular processes, including DNA replication, transcription, protein homeostasis and cell metabolism. We suggest that the network core, consisting of genes mutually regulated by their intragenic miRNAs, could coordinate adjacent pathways or homeostatic control circuits, serving as a horizontal inter-circuit link. Notably, expression patterns of these genes had an efficient prognostic potential for breast and colorectal cancer patients.

Added: Oct 7, 2020
Article
Galatenko V. V., Galatenko A. V., Samatov T. et al. Scientific Reports. 2018. Vol. 8.

MicroRNAs (miRNAs) are a family of short noncoding RNAs that posttranscriptionally regulate gene expression and play an important role in multiple cellular processes. A significant percentage of miRNAs are intragenic, which is often functionally related to their host genes playing either antagonistic or synergistic roles. In this study, we constructed and analyzed the entire network of intergenic interactions induced by intragenic miRNAs. We further focused on the core of this network, which was defined as a union of nontrivial strongly connected components, i.e., sets of nodes (genes) mutually connected via directed paths. Both the entire network and its core possessed statistically significant non-random properties. Specifically, genes forming the core had high expression levels and low expression variance. Furthermore, the network core did not split into separate components corresponding to individual signalling or metabolic pathways, but integrated genes involved in key cellular processes, including DNA replication, transcription, protein homeostasis and cell metabolism. We suggest that the network core, consisting of genes mutually regulated by their intragenic miRNAs, could coordinate adjacent pathways or homeostatic control circuits, serving as a horizontal inter-circuit link. Notably, expression patterns of these genes had an efficient prognostic potential for breast and colorectal cancer patients.

Added: Oct 31, 2020
Article
Kovaleva N., Kusmartsev F., Mekhiya A. et al. Scientific Reports. 2020. Vol. 10. P. 21172.

Localisation phenomena in highly disordered metals close to the extreme conditions determined by the Mott-Ioffe-Regel (MIR) limit when the electron mean free path is approximately equal to the interatomic distance is a challenging problem. Here, to shed light on these localisation phenomena, we studied the dc transport and optical conductivity properties of nanoscaled multilayered films composed of disordered metallic Ta and magnetic FeNi nanoisland layers, where ferromagnetic FeNi nanoislands have giant magnetic moments of 10^3–10^5 Bohr magnetons (μB ). In these multilayered structures, FeNi nanoisland giant magnetic moments are interacting due to the indirect exchange forces acting via the Ta electron subsystem. We discovered that the localisation phenomena in the disordered Ta layer lead to a decrease in the Drude contribution of free charge carriers and the appearance of the low-energy electronic excitations in the 1–2 eV spectral range characteristic of electronic correlations, which may accompany the formation of electronic inhomogeneities. From the consistent results of the dc transport and optical studies we found that with an increase in theFeNi layer thickness across the percolation threshold evolution from the superferromagnetic to ferromagnetic behaviour within the FeNi layer leads to the delocalisation of Ta electrons from the associated localised electronic states. On the contrary, we discovered that when the FeNi layer is discontinuous and represented by randomly distributed superparamagnetic FeNi nanoislands, the Ta layer normalized dc conductivity falls down below the MIR limit by about 60%. The discovered effect leading to the dc conductivity fall below the MIR limit can be associated with non-ergodicity and purely quantum (many-body) localisation phenomena, which need to be challenged further

Added: Dec 7, 2020
Article
Gorin A., Krugliakova E., Nikulin V. et al. Scientific Reports. 2020. Vol. 10. No. 21161. P. 1-14.

Both human and animal studies have demonstrated remarkable findings of experience-induced plasticity in the cortex. Here, we investigated whether the widely used monetary incentive delay (MID) task changes the neural processing of incentive cues that code expected monetary outcomes. We used a novel auditory version of the MID task, where participants responded to acoustic cues that coded expected monetary losses. To investigate task-induced brain plasticity, we presented incentive cues as deviants during passive oddball tasks before and after two sessions of the MID task. During the oddball task, we recorded the mismatch-related negativity (MMN) as an index of cortical plasticity. We found that two sessions of the MID task evoked a significant enhancement of MMN for incentive cues that predicted large monetary losses, specifically when monetary cue discrimination was essential for maximising monetary outcomes. The task-induced plasticity correlated with the learning-related neural activity recorded during the MID task. Thus, our results confirm that the auditory processing of (loss) incentive cues is dynamically modulated by previous monetary outcomes

Added: Oct 30, 2020
Article
Kenville R., Maudrich T., Vidaurre C. et al. Scientific Reports. 2020. Vol. 10. No. 1. P. 5021.

While much is known about motor control during simple movements, corticomuscular communication profiles during compound movement control remain largely unexplored. Here, we aimed at examining frequency band related interactions between brain and muscles during different movement periods of a bipedal squat (BpS) task utilizing regression corticomuscular coherence (rCMC), as well as partial directed coherence (PDC) analyses. Participants performed 40 squats, divided into three successive movement periods (Eccentric (ECC), Isometric (ISO) and Concentric (CON)) in a standardized manner. EEG was recorded from 32 channels specifically-tailored to cover bilateral sensorimotor areas while bilateral EMG was recorded from four main muscles of BpS. We found both significant CMC and PDC (in beta and gamma bands) during BpS execution, where CMC was significantly elevated during ECC and CON when compared to ISO. Further, the dominant direction of information flow (DIF) was most prominent in EEG-EMG direction for CON and EMG-EEG direction for ECC. Collectively, we provide novel evidence that motor control during BpS is potentially achieved through central motor commands driven by a combination of directed inputs spanning across multiple frequency bands. These results serve as an important step toward a better understanding of brain-muscle relationships during multi joint compound movements.

Added: Sep 15, 2020
Article
Beknazarov N., Jin S., Poptsova M. Scientific Reports. 2020. Vol. 10. P. 19134.

Computational methods to predict Z-DNA regions are in high demand to understand the functional role of Z-DNA. The previous state-of-the-art method Z-Hunt is based on statistical mechanical and energy considerations about B- to Z-DNA transition using sequence information. Z-DNA CHiP-seq experiment results showed little overlap with Z-Hunt predictions implying that sequence information only is not sufficient to explain emergence of Z-DNA at different genomic locations. Adding epigenetic and other functional genomic mark-ups to DNA sequence level can help revealing the functional Z-DNA sites. Here we take advantage of the deep learning approach that can analyze and extract information from large volumes of molecular biology data. We developed a machine learning approach DeepZ that aggregates information from genome-wide maps of epigenetic markers, transcription factor and RNA polymerase binding sites, and chromosome accessibility maps. With the developed model we not only verify the experimental Z-DNA predictions, but also generate the whole-genome annotation, introducing new possible Z-DNA regions, which have not yet been found in experiments and can be of interest to the researchers from various fields.

Added: Dec 11, 2020
Article
Beknazarov N., Jin S., Poptsova M. Scientific Reports. 2020.

Computational methods to predict Z-DNA regions are in high demand to understand the functional role of Z-DNA. The previous state-of-the-art method Z-Hunt is based on statistical mechanical and energy considerations about B- to Z-DNA transition using sequence information. Z-DNA CHiP-seq experiment results showed little overlap with Z-Hunt predictions implying that sequence information only is not sufficient to explain emergence of Z-DNA at different genomic locations. Adding epigenetic and other functional genomic mark-ups to DNA sequence level can help revealing the functional Z-DNA sites. Here we take advantage of the deep learning approach that can analyze and extract information from large volumes of molecular biology data. We developed a machine learning approach DeepZ that aggregates information from genome-wide maps of epigenetic markers, transcription factor and RNA polymerase binding sites, and chromosome accessibility maps. With the developed model we not only verify the experimental Z-DNA predictions, but also generate the whole-genome annotation, introducing new possible Z-DNA regions, which have not yet been found in experiments and can be of interest to the researchers from various fields.

Added: Mar 9, 2021
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
Bräuer J., Blasi D. Scientific Reports. 2021. Vol. 11. P. 1-10.

Most current knowledge about dogs’ understanding of, and reacting to, their environment is limited to the visual or auditory modality, but it remains unclear how olfaction and cognition are linked together. Here we investigate how domestic dogs search for their owners using their excellent olfactory sense. We raise the question whether dogs have a representation of someone when they smell their track. The question is what they expect when they follow a trail or whether they perceive an odour as a relevant or non-relevant stimulus. We adopted a classical violation-of-expectation paradigm—and as targets we used two persons that were both important to the dog, usually the owners. In the critical condition subjects could track the odour trail of one target, but at the end of the trail they find another target. Dogs showed an increased activity when the person did not correspond with the trail compared to a control condition. Moreover, we found huge individual differences in searching behaviour supporting the assumption that dogs are only able to smell when they really sniff, and that the temperature has an influence on dogs performance. Results are discussed in the light of how cognitive abilities, motivation and odour perception influence each other.

Added: Mar 3, 2021