• A
  • A
  • A
  • ABC
  • ABC
  • ABC
  • А
  • А
  • А
  • А
  • А
Regular version of the site
Of all publications in the section: 69
Sort:
by name
by year
Article
Gnuchikh E., Baranova A., Schukina V. et al. Plos One. 2019. Vol. 14. No. 12. P. 1-11.

Here we present a study of the thermal inactivation and the refolding of the proteins in Gram positive Bacillus subtilis. To enable use of bacterial luciferases as the models for protein thermal inactivation and refolding in B. subtilis cells, we developed a variety of bright luminescent B. subtilis strains which express luxAB genes encoding luciferases of differing thermolability. The kinetics of the thermal inactivation and the refolding of luciferases from Photorhabdus luminescens and Photobacterium leiognathi were compared in Gram negative and Gram positive bacteria. In B. subtilis cells, these luciferases are substantially more thermostable than in Escherichia coli. Thermal inactivation of the thermostable luciferase P. luminescens in B. subtilis at 48.5°C behaves as a first-order reaction. In E.coli, the first order rate constant (Kt) of the thermal inactivation of luciferase in E. coli exceeds that observed in B. subtilis cells 2.9 times. Incubation time dependence curves for the thermal inactivation of the thermolabile luciferase of P. leiognathi luciferase in the cells of E. coli and B. subtilis may be described by first and third order kinetics, respectively. Here we shown that the levels and the rates of refolding of thermally inactivated luciferases in B. subtilis cells are substantially lower that that observed in E. coli. In dnaK-negative strains of B. subtilis, both the rates of thermal inactivation and the efficiency of refolding are similar to that observed in wild-type strains. These experiments point that the role that DnaKJE plays in thermostability of luciferases may be limited to bacterial species resembling E. coli. 

Added: Feb 26, 2020
Article
Blythe D. A., Nikulin V. Plos One. 2017. Vol. 12. No. 5. P. 1-28.

We show theoretically that the hypothesis of criticality as a theory of long-range fluctuation in the human brain may be distinguished from the theory of passive filtering on the basis of macroscopic neuronal signals such as the electroencephalogram, using novel theory of narrowband amplitude time-series at criticality. Our theory predicts the division of critical activity into meta-universality classes. As a consequence our analysis shows that experimental electroencephalography data favours the hypothesis of criticality in the human brain.

Added: Jun 7, 2017
Article
Rudnev M., Vauclair C., Bastian B. Plos One. 2020. Vol. 15. No. 6. P. 1-11.

Moral vitalism refers to a tendency to view good and evil as actual forces that can influence people and events. The Moral Vitalism Scale had been designed to assess moral vitalism in a brief survey form. Previous studies established the reliability and validity of the scale in US-American and Australian samples. In this study, the cross-cultural comparability of the scale was tested across 28 different cultural groups worldwide through measurement invariance tests. A series of exact invariance tests marginally supported partial metric invariance, however, an approximate invariance approach provided evidence of partial scalar invariance for a 5-item measure. The established level of measurement invariance allows for comparisons of latent means across cultures. We conclude that the brief measure of moral vitalism is invariant across 28 cultures and can be used to estimate levels of moral vitalism with the same precision across very different cultural settings.

Added: Jun 21, 2020
Article
Kolbeneva M. G., Alexandrov Y. Plos One. 2016. Vol. 11. No. 7. P. 1-37.

Language acquisition is based on our knowledge about the world and forms through multi- ple sensory-motor interactions with the environment. We link the properties of individual experience formed at different stages of ontogeny with the phased development of sensory modalities and with the acquisition of words describing the appropriate forms of sensitivity. To test whether early-formed experience related to skin sensations, olfaction and taste differs from later-formed experience related to vision and hearing, we asked Russian- speaking participants to categorize or to assess the pleasantness of experience mentally reactivated by sense-related adjectives found in common dictionaries. It was found that cat- egorizing adjectives in relation to vision, hearing and skin sensations took longer than cate- gorizing adjectives in relation to olfaction and taste. In addition, experience described by adjectives predominantly related to vision, hearing and skin sensations took more time for the pleasantness judgment and generated less intense emotions than that described by adjectives predominantly related to olfaction and taste. Interestingly the dynamics of skin resistance corresponded to the intensity and pleasantness of reported emotions. We also found that sense-related experience described by early-acquired adjectives took less time for the pleasantness judgment and generated more intense and more positive emotions than that described by later-acquired adjectives. Correlations were found between the time of the pleasantness judgment of experience, intensity and pleasantness of reported emo- tions, age of acquisition, frequency, imageability and length of sense-related adjectives. All in all these findings support the hypothesis that early-formed experience is less differenti- ated than later-formed experience. 

Added: Aug 24, 2016
Article
Pokhoday M., Scheepers C., Shtyrov Y. et al. Plos One. 2018. Vol. 13. No. 4. P. 1-12.

Understanding the determinants of syntactic choice in sentence production is a salient topic in psycholinguistics. Existing evidence suggests that syntactic choice results from an interplay between linguistic and non-linguistic factors, and a speaker’s attention to the elements of a described event represents one such factor. Whereas multimodal accounts of attention suggest a role for different modalities in this process, existing studies examining attention effects in syntactic choice are primarily based on visual cueing paradigms. Hence, it remains unclear whether attentional effects on syntactic choice are limited to the visual modality or are indeed more general. This issue is addressed by the current study. Native English participants viewed and described line drawings of simple transitive events while their attention was directed to the location of the agent or the patient of the depicted event by means of either an auditory (monaural beep) or a motor (unilateral key press) lateral cue. Our results show an effect of cue location, with participants producing more passive-voice descriptions in the patient-cued conditions. Crucially, this cue location effect emerged in the motor-cue but not (or substantially less so) in the auditory-cue condition, as confirmed by a reliable interaction between cue location (agent vs. patient) and cue type (auditory vs. motor). Our data suggest that attentional effects on the speaker’s syntactic choices are modality-specific and limited to the visual and motor, but not the auditory, domain.

Added: Mar 29, 2018
Article
Petushkova N., Zgoda V., Pyatnitskiy M. et al. Plos One. 2017. Vol. 12. No. 5. P. 0177427-1-0177427-21.

Liquid chromatography-tandem mass spectrometry was used to analyze plasma proteins of volunteers (control) and patients with glioblastoma multiform (GBM). A database search was pre-set with a variable post-translational modification (PTM): phosphorylation, acetylation or ubiquitination. There were no significant differences between the control and the GBM groups regarding the number of protein identifications, sequence coverage or number of PTMs. However, in GBM plasma, we unambiguously observed a decreased fraction in post-translationally modified peptides identified with high quality. The disease-specific PTM patterns were extracted and mapped to the set of FDA-approved plasma protein markers. Decreases of 46% and 24% in the number of acetylated and ubiquitinated peptides, respectively, were observed in the GBM samples. Significance of capturing disease-associated patterns of protein modifications was envisaged.

Added: Mar 14, 2018
Article
Charkhabi M., Халезов Е. А., Kotova T. et al. Plos One. 2019. Vol. 14. No. 11. P. 1-13.

School engagement reflects the degree to which students are invested, motivated and willing to participate in learning at their school and this relates to future academic and professional success. Although school engagement is a primary factor predicting educational dropout or successful school completion in Europe and North America, little is known about school engagement factors in non-English speaking countries. We adapted a 15-item school engagement scale and assessed validity and reliability of the Russian translation on a sample of Russian school-aged children (N = 537, 6-12 years, 46% females) who attended at public schools in Moscow. Results of the final factorial structure that included emotional, cognitive and behavioral components were selected based on its excellent fit indices and principles of parsimony. Component results show that the emotional component has the highest internal consistency and the behavioral component has the lowest. Although, all components are significantly interrelated, we observed no gender differences and no significant correlation with age. Theoretically, our data agree with the notion that children's emotional engagement in schools sets the foundation for learning, participating and succeeding in school activities. Practically, the proposed scale in Russian can be used in educational and clinical settings with Russian speaking children. our data agree with the notion that children's emotional engagement in schools sets the foundation for learning, participating and succeeding in school activities. Practically, the proposed scale in Russian can be used in educational and clinical settings with Russian speaking children. our data agree with the notion that children's emotional engagement in schools sets the foundation for learning, participating and succeeding in school activities. Practically, the proposed scale in Russian can be used in educational and clinical settings with Russian speaking children.

Added: Oct 30, 2019
Article
Smirnov I. Plos One. 2019. Vol. 14. No. 5. P. 1-9.

The Internet provides students with a unique opportunity to connect and maintain social ties with peers from other schools, irrespective of how far they are from each other. However, little is known about the real structure of such online relationships. In this paper, we investigate the structure of interschool friendship on a popular social networking site. We use data from 36, 951 students from 590 schools of a large European city. We find that the probability of a friendship tie between students from neighboring schools is high and that it decreases with the distance between schools following the power law. We also find that students are more likely to be connected if the educational outcomes of their schools are similar. We show that this fact is not a consequence of residential segregation. While high- and low-performing schools are evenly distributed across the city, this is not the case for the digital space, where schools turn out to be segregated by educational outcomes. There is no significant correlation between the educational outcomes of a school and its geographical neighbors; however, there is a strong correlation between the educational outcomes of a school and its digital neighbors. These results challenge the common assumption that the Internet is a borderless space, and may have important implications for the understanding of educational inequality in the digital age.

Added: May 29, 2019
Article
Bulla I., Spicknall I., Gromov Dmitry et al. Plos One. 2018. No. e0204741. P. 1-19.

Predicting the population-level effects of an infectious disease intervention that incorporate multiple modes of intervention is complicated by the joint non-linear dynamics of both infection transmission and the intervention itself. In this paper, we consider the sensitivity of Dynamic Optimal Control Profiles (DOCPs) for the optimal joint investment in both a contagiousness and susceptibility-based control of HIV to bio-behavioral, economic, and programmatic assumptions. The DOCP is calculated using recently developed numerical algorithms that allow controls to be represented by a set of piecewise constant functions that maintain a constant yearly budget. Our transmission model assumes multiple stages of HIV infection corresponding to acute and chronic infection and both within- and between-individual behavioral heterogeneity. We parameterize a baseline scenario from a longitudinal study of sexual behavior in MSM and consider sensitivity of the DOCPs to deviations from that baseline scenario. In the baseline scenario, the primary determinant of the dominant control were programmatic factors, regardless of budget. In sensitivity analyses, the qualitative aspects of the optimal control policy were often robust to significant deviation in assumptions regarding transmission dynamics. In addition, we found several conditions in which long-term joint investment in both interventions was optimal. Our results suggest that modeling in the service of decision support for intervention design can improve population-level effects of a limited set of economic resources. We found that economic and programmatic factors were as important as the inherent transmission dynamics in determining population-level intervention effects. Given our finding that the DOCPs were robust to alternative biological and behavioral assumptions it may be possible to identify DOCPs even when the data are not sufficient to identify a transmission model.

Added: Oct 8, 2019
Article
Oksuzyan A., Shkolnikova M., Vaupel J. et al. Plos One. 2015. Vol. 10. No. 6.
Added: Jun 21, 2017
Article
Sircova A., Karimi F., Osin E. N. et al. Plos One. 2015. Vol. 10. No. 3. P. e0117612.

In a situation with a limited common resource, cooperation between individuals sharing the resource is essential. However, people often act upon self-interest in irrational ways that threaten the long-term survival of the whole group. A lack of sustainable or environmentally responsible behavior is often observed. In this study, we examine how the maximization of benefits principle works in a wider social interactive context of personality preferences, in order to gain a more realistic insight into the evolution of cooperation. We used time perspective (TP), a concept reflecting individual differences in orientation towards past, present, or future, and relevant for making sustainable choices. We developed a personality-driven agent-based model that explores the role of personality in the outcomes of social dilemmas and includes multiple facets of diversity. 1) The agents have different behavior strategies: individual differences derived by applying cluster analysis to survey data from 22 countries (N=10,940) and resulting in 7 cross-cultural profiles of TP. 2) The non-uniform distribution of the types of agents across countries. 3) The diverse interactions between the agents and 4) diverse responses to those interactions in a well-mixed population. As one of the results, we introduced an index of overall cooperation for each of the 22 countries, which was validated against cultural, economic, and sustainability indicators (HDI, dimensions of national culture, and Environment Performance Index). It was associated with higher human development, higher individualism, lower power distance, and better environmental performance. The findings illustrate how individual differences in TP can be simulated to predict the ways people in different countries solve the personal vs common gain dilemma in the global limited-resource situation. This inter-disciplinary approach to social simulation can be adopted to explain the possible causes of global environmental issues and to predict their possible outcomes.

Added: Dec 24, 2014
Article
Hahn J., Tsoy O. V., Thalmann S. et al. Plos One. 2016. No. 11(10). P. e0165429-1-e0165429-24.

Small open reading frames (sORFs) and genes for non-coding RNAs are poorly investigated components of most genomes. Our analysis of 1391 ORFs recently annotated in the soybean symbiont Bradyrhizobium japonicum USDA 110 revealed that 78% of them contain less than 80 codons. Twenty-one of these sORFs are conserved in or outside Alphaproteobacteria and most of them are similar to genes found in transposable elements, in line with their broad distribution. Stabilizing selection was demonstrated for sORFs with proteomic evidence and bll1319_ISGA which is conserved at the nucleotide level in 16 alphaproteobacterial species, 79 species from other taxa and 49 other Proteobacteria. Further we used Northern blot hybridization to validate ten small RNAs (BjsR1 to BjsR10) belonging to new RNA families. We found that BjsR1 and BjsR3 have homologs outside the genus Bradyrhizobium, and BjsR5, BjsR6, BjsR7, and BjsR10 have up to four imperfect copies in Bradyrhizobium genomes. BjsR8, BjsR9, and BjsR10 are present exclusively in nodules, while the other sRNAs are also expressed in liquid cultures. We also found that the level of BjsR4 decreases after exposure to tellurite and iron, and this down-regulation contributes to survival under high iron conditions. Analysis of additional small RNAs overlapping with 3’-UTRs revealed two new repetitive elements named Br-REP1 and Br-REP2. These REP elements may play roles in the genomic plasticity and gene regulation and could be useful for strain identification by PCR-fingerprinting. Furthermore, we studied two potential toxin genes in the symbiotic island and confirmed toxicity of the yhaVhomolog bll1687 but not of the newly annotated higB homolog blr0229_ISGA in E. coli. Finally, we revealed transcription interference resulting in an antisense RNA complementary to blr1853, a gene induced in symbiosis. The presented results expand our knowledge on sORFs, non-coding RNAs and repetitive elements in B. japonicum and related bacteria.

Added: Dec 2, 2016
Article
Мягков М. Г., Berkman E. T., Lukinova E. et al. Plos One. 2015. Vol. 10. No. 3. P. 1-18.

In the recent literature, several hypotheses have been offered to explain patterns of human behavior in social environments. In particular, these patterns include ‘prosocial’ ones, such as fairness, cooperation, and collective good provision. Psychologists suggest that these prosocial behaviors are driven not by miscalculations, but by salience of social identity, in-group favoritism, emotion, or evolutionary adaptations. This paper imports psychology scholarship into an economic model and results in a sustainable solution to collective action problems without any external enforcement mechanisms. This natural mechanism of public goods provision is created, analyzed, and observed in a controlled laboratory environment using experimental techniques.

Added: Oct 31, 2018
Article
Iscan Z., Nikulin V. Plos One. 2018. Vol. 13. No. 1. P. 1-17.

Brain-computer interface (BCI) paradigms are usually tested when environmental and biological artifacts are intentionally avoided. In this study, we deliberately introduced different perturbations in order to test the robustness of a steady state visual evoked potential (SSVEP) based BCI. Specifically we investigated to what extent a drop in performance is related to the degraded quality of EEG signals or rather due to increased cognitive load. In the online tasks, subjects focused on one of the four circles and gave feedback on the correctness of the classification under four conditions randomized across subjects: Control (no perturbation), Speaking (counting loudly and repeatedly from one to ten), Thinking (mentally counting repeatedly from one to ten), and Listening (listening to verbal counting from one to ten). Decision tree, Naïve Bayes and K-Nearest Neighbor classifiers were used to evaluate the classification performance using features generated by canonical correlation analysis. During the online condition, Speaking and Thinking decreased moderately the mean classification accuracy compared to Control condition whereas there was no significant difference between Listening and Control conditions across subjects. The performances were sensitive to the classification method and to the perturbation conditions. We have not observed significant artifacts in EEG during perturbations in the frequency range of interest except in theta band. Therefore we concluded that the drop in the performance is likely to have a cognitive origin. During the Listening condition relative alpha power in a broad area including central and temporal regions primarily over the left hemisphere correlated negatively with the performance thus most likely indicating active suppression of the distracting presentation of the playback. This is the first study that systematically evaluates the effects of natural artifacts (i.e. mental, verbal and audio perturbations) on SSVEP-based BCIs. The results can be used to improve individual classification performance taking into account effects of perturbations.

Added: Oct 30, 2018
Article
Ossadtchi A. Plos One. 2018. P. 1-15.

We utilized the event-related potential (ERP) technique to study neural activity associated with different levels of working memory (WM) load during simultaneous interpretation (SI) of continuous prose. The amplitude of N1 and P1 components elicited by task-irrelevant tone probes was significantly modulated as a function of WM load but not the direction of interpretation. Furthermore, the latency of the P1 increased significantly with WM load. The WM load effect on N1 latency, however, did not reach significance. Larger negativity under lower WM loads suggests that more attention is available to process the source message, providing the first electrophysiological evidence in support of the Efforts Model of SI. Relationships between the direction of interpretation and median WM load are also discussed.

Added: Nov 30, 2018
Article
Koshkin R., Shtyrov Y., Myachykov A. et al. Plos One. 2018. Vol. 10. No. 13. P. 1-18.

We utilized the event-related potential (ERP) technique to study neural activity associated with different levels of working memory (WM) load during simultaneous interpretation (SI) of continuous prose. The amplitude of N1 and P1 components elicited by task-irrelevant tone probes was significantly modulated as a function of WM load but not the direction of interpretation. Furthermore, the latency of the P1 increased significantly with WM load. The WM load effect on N1 latency, however, did not reach significance. Larger negativity under lower WM loads suggests that more attention is available to process the source message, providing the first electrophysiological evidence in support of the Efforts Model of SI. Relationships between the direction of interpretation and median WM load are also discussed.

Added: Nov 1, 2018
Article
Nye J. V., Al-Ubaydli O., Houser D. et al. Plos One. 2013. Vol. 8. No. 3.

We report data from laboratory experiments where participants were primed using phrases related to markets and trade. Participants then participated in trust games with anonymous strangers. The decisions of primed participants are compared to those of a control group. We find evidence that priming for market participation affects positively the beliefs regarding the trustworthiness of anonymous strangers and increases trusting decisions.

Added: Mar 28, 2013
Article
Kurnosov A., Ustyugova S., Nazarov V. et al. Plos One. 2015. Vol. 10. No. 2. P. e0117854.

Retroelement activity is a common source of polymorphisms in human genome. The mechanism whereby retroelements contribute to the intraindividual genetic heterogeneity by inserting into the DNA of somatic cells is gaining increasing attention. Brain tissues are suspected to accumulate genetic heterogeneity as a result of the retroelements somatic activity. This study aims to expand our understanding of the role retroelements play in generating somatic mosaicism of neural tissues. Whole-genome Alu and L1 profiling of genomic DNA extracted from the cerebellum, frontal cortex, subventricular zone, dentate gyrus, and the myocardium revealed hundreds of somatic insertions in each of the analyzed tissues. Interestingly, the highest concentration of such insertions was detected in the dentate gyrus—the hotspot of adult neurogenesis. Insertions of retroelements and their activity could produce genetically diverse neuronal subsets, which can be involved in hippocampal-dependent learning and memory.

Added: Feb 19, 2015
Article
Grigoriev P., Andreev E. M. Plos One. 2015. Vol. 10. No. 9.

Background and Aim Harmful alcohol consumption has long been recognized as being the major determinant of male premature mortality in the European countries of the former USSR. Our focus here is on Belarus and Russia, two Slavic countries which continue to suffer enormously from the burden of the harmful consumption of alcohol. However, after a long period of deterioration, mortality trends in these countries have been improving over the past decade. We aim to investigate to what extent the recent declines in adult mortality in Belarus and Russia are attributable to the anti-alcohol measures introduced in these two countries in the 2000s. Data and Methods We rely on the detailed cause-specific mortality series for the period 1980–2013. Our analysis focuses on the male population, and considers only a limited number of causes of death which we label as being alcohol-related: accidental poisoning by alcohol, liver cirrhosis, ischemic heart diseases, stroke, transportation accidents, and other external causes. For each of these causes we computed age-standardized death rates. The life table decomposition method was used to determine the age groups and the causes of death responsible for changes in life expectancy over time. Conclusion Our results do not lead us to conclude that the schedule of anti-alcohol measures corresponds to the schedule of mortality changes. The continuous reduction in adult male mortality seen in Belarus and Russia cannot be fully explained by the anti-alcohol policies implemented in these countries, although these policies likely contributed to the large mortality reductions observed in Belarus and Russia in 2005–2006 and in Belarus in 2012. Thus, the effects of these policies appear to have been modest. We argue that the antialcohol measures implemented in Belarus and Russia simply coincided with fluctuations in alcohol-related mortality which originated in the past. If these trends had not been underway already, these huge mortality effects would not have occurred.

Added: Sep 24, 2015
Article
Schoors K., Hoefman K., Bramson A. et al. Plos One. 2018. Vol. 13. No. 11. P. 1-12.

According to hedonic pricing theory (HPT) market forces operate on individual characteristics of a good, and the price of a product is the aggregate of the price across those characteristics. The relationship between price and characteristics remains poorly understood because characteristic qualities are hard to quantify, people have varying levels of information about characteristics, and people have heterogeneous preferences over characteristics. By analyzing data from a large, market-driven virtual world we are able to test HPT, while largely avoiding these pitfalls. We find that a linear model with functional characteristics predicts the prices poorly, but a log-linear model performs quite well. Adding social characteristics to this log-linear model improves the predictions substantially. This work strongly supports HPT and demonstrates a “rational” calculus including social value.

Added: May 31, 2019
Article
Saygitov RT. Plos One. 2014. Vol. 9. No. 1. P. e86969.

The impact of grants on research productivity has been investigated by a number of retrospective studies. The results of these studies vary considerably. The objective of my study was to investigate the impact of funding through the RF President’s grants for young scientists on the research productivity of awarded applicants. The study compared the number of total articles and citations for awarded and rejected applicants who in 2007 took part in competitions for young candidates of science (CoS’s) and doctors of science (DoS’s) in the scientific field of medicine. The bibliometric analysis was conducted for the period from 2003 to 2012 (five years before and after the competition). The source of bibliometric data is the eLIBRARY.RU database. The impact of grants on the research productivity of Russian young scientists was assessed using the meta-analytical approach based on data from quasi-experimental studies conducted in other countries. The competition featured 149 CoS’s and 41 DoS’s, out of which 24 (16%) and 22 (54%) applicants, respectively, obtained funding. No difference in the number of total articles and citations at baseline, as well as in 2008–2012, for awarded and rejected applicants was found. The combination of data from the Russian study and other quasi-experimental studies (6 studies, 10 competitions) revealed a small treatment effect – an increase in the total number of publications over a 4–5-year period after the competition by 1.23 (95% CI 0.48–1.97). However, the relationship between the number of total publications published by applicants before and after the competition revealed that this treatment effect is an effect of the “maturation” of scientists with a high baseline publication activity – not of grant funding.

Added: Apr 25, 2014