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Of all publications in the section: 84
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Article
Dokuka S., Valeeva D., Yudkevich M. M. Plos One. 2020. Vol. 15. No. 7. P. e0236737.

Behavior diffusion through social networks is a key social process. It may be guided by various factors such as network topology, type of propagated behavior, and the strength of network connections. In this paper, we claim that the type of social interactions is also an important ingredient of behavioral diffusion. We examine the spread of academic achievements of first-year undergraduate students through friendship and study assistance networks, applying stochastic actor-oriented modeling. We show that informal social connections transmit performance while instrumental connections do not. The results highlight the importance of friendship in educational environments and contribute to debates on the behavior spread in social networks.

 

Added: Jul 27, 2020
Article
Thiel S. D., Bitzer S., Nierhaus T. et al. Plos One. 2014. Vol. 2. No. 9. P. e89802.

Perceptual decisions not only depend on the incoming information from sensory systems but constitute a combination of current sensory evidence and internally accumulated information from past encounters. Although recent evidence emphasizes the fundamental role of prior knowledge for perceptual decision making, only few studies have quantified the relevance of such priors on perceptual decisions and examined their interplay with other decision-relevant factors, such as the stimulus properties. In the present study we asked whether hysteresis, describing the stability of a percept despite a change in stimulus property and known to occur at perceptual thresholds, also acts as a form of an implicit prior in tactile spatial decision making, supporting the stability of a decision across successively presented random stimuli (i.e., decision hysteresis). We applied a variant of the classical 2-point discrimination task and found that hysteresis influenced perceptual decision making: Participants were more likely to decide 'same' rather than 'different' on successively presented pin distances. In a direct comparison between the influence of applied pin distances (explicit stimulus property) and hysteresis, we found that on average, stimulus property explained significantly more variance of participants' decisions than hysteresis. However, when focusing on pin distances at threshold, we found a trend for hysteresis to explain more variance. Furthermore, the less variance was explained by the pin distance on a given decision, the more variance was explained by hysteresis, and vice versa. Our findings suggest that hysteresis acts as an implicit prior in tactile spatial decision making that becomes increasingly important when explicit stimulus properties provide decreasing evidence.

Added: Oct 23, 2014
Article
Korostelev Y., Zharov I., Mironov A. A. et al. Plos One. 2016. Vol. 11. No. 9. P. 1-23.

The large and increasing volume of genomic data analyzed by comparative methods provides information about transcription factors and their binding sites that, in turn, enables statistical analysis of correlations between factors and sites, uncovering mechanisms and evolution of specific protein-DNA recognition. Here we present an online tool, Prot-DNA-Korr, designed to identify and analyze crucial protein-DNA pairs of positions in a family of transcription factors. Correlations are identified by analysis of mutual information between columns of protein and DNA alignments. The algorithm reduces the effects of common phylogenetic history and of abundance of closely related proteins and bindingsites. We apply it to five closely related subfamilies of the MerR family of bacterial transcription factors that regulate heavy metal resistance systems. We validate the approach using known 3D structures of MerR-family proteins in complexes with their cognate DNA binding sitesand demonstrate that a significant fraction of correlated positions indeed form specific side-chain-to-base contacts. The joint distribution of amino acids and nucleotides hence may be used to predict changes of specificity for point mutations in transcription factors.

Added: Mar 14, 2018
Article
Grigoriev P., Jasilionis D., Stumbrys D. et al. Plos One. 2017. Vol. 12. No. 7. P. 1-14.

Although excessive alcohol-related mortality in the post-Soviet countries remains the major public health threat, determinants of this phenomenon are still poorly understood. We assess simultaneously individual- and area-level factors associated with an elevated risk of alcohol-related mortality among Lithuanian males aged 30–64.

Added: Oct 25, 2017
Article
Nersisyan S., Shkurnikov M., Turchinovich A. et al. Plos One. 2020. Vol. 15. No. 7. P. e0235987.

Development of novel approaches for regulating the expression of angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2) is becoming increasingly important within the context of the ongoing COVID-19 pandemic since these enzymes play a crucial role in cell infection. In this work we searched for putative ACE2 and TMPRSS2 expression regulation networks mediated by various miRNA isoforms (isomiR) across different human organs using publicly available paired miRNA/mRNA-sequencing data from The Cancer Genome Atlas (TCGA) project. As a result, we identified several miRNA families targeting ACE2 and TMPRSS2 genes in multiple tissues. In particular, we found that lysine-specific demethylase 5B (JARID1B), encoded by the KDM5B gene, can indirectly affect ACE2 / TMPRSS2 expression by repressing transcription of hsa-let-7e / hsa-mir-125a and hsa-mir-141 / hsa-miR-200 miRNA families which are targeting these genes.

Added: Jul 29, 2020
Article
Hennig-Schmidt H., Goerg S., Walkowitz G. et al. Plos One. 2016. Vol. 11. No. 6. P. 1-16.

The reconcilability of actions and beliefs in inter-country relationships, either in business or politics, is of vital importance as incorrect beliefs on foreigners’ behavior can have serious implications. We study a typical inter-country interaction by means of a controlled laboratory investment game experiment in Germany, Israel and Palestine involving 400 student participants in total. An investor has to take a risky decision in a foreign country that involves transferring money to an investee/allocator. We found a notable constellation of calibrated and un-calibrated beliefs. Within each country, transfer standards exist, which investees correctly anticipate within their country. However, across countries these standards differ. By attributing the standard of their own environment to the other countries investees are remarkably bad in predicting foreign investors’ behavior. The tendency to ignore this potential difference can be a source of misinterpreting motives in cross-country interaction. Foreigners might perceive behavior as unfavorable or favorable differentiation, even though – unknown to them – investors actually treat fellow-country people and foreigners alike.

Added: Oct 4, 2018
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
Ernst A., Putscher A., Samatov T. R. et al. Plos One. 2018. Vol. 13. No. 2.

Finding additional functional targets for combination therapy could improve the outcome for melanoma patients. In a spontaneous metastasis xenograft model of human melanoma a shRNA mediated knockdown of L1CAM more than sevenfold reduced the number of lung metastases after the induction of subcutaneous tumors for two human melanoma cell lines (MeWo, MV3). Whole genome expression arrays of the initially L1CAM high MeWo subcutaneous tumors revealed unchanged or downregulated genes involved in epithelial to mesenchymal transition (EMT) except an upregulation of Jagged 1, indicating a compensatory change in Notch signaling especially as Jagged 1 expression showed an increase in MeWo L1CAM metastases and Jagged 1 was expressed in metastases of the initially L1CAM low MV3 cells as well. Expression of 17 genes showed concordant regulation for L1CAM knockdown tumors of both cell lines. The changes in gene expression indicated changes in the EMT network of the melanoma cells and an increase in p53/p21 and p38 activity contributing to the reduced metastatic potential of the L1CAM knockdowns. Taken together, these data make L1CAM a highly interesting therapeutic target to prevent further metastatic spread in melanoma patients.

Added: Feb 1, 2021
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
Lopukhina A., Lopukhin K., Laurinavichyute A. Plos One. 2021. Vol. 16. No. 1. P. 1-26.

During reading or listening, people can generate predictions about the lexical and morphosyntactic properties of upcoming input based on available context. Psycholinguistic experiments that study predictability or control for it conventionally rely on a human-based approach and estimate predictability via the cloze task. Our study investigated an alternative corpus-based approach for estimating predictability via language predictability models. We obtained cloze and corpus-based probabilities for all words in 144 Russian sentences, correlated the two measures, and found a strong correlation between them. Importantly, we estimated how much variance in eye movements registered while reading the same sentences was explained by each of the two probabilities and whether the two probabilities explain the same variance. Along with lexical predictability (the activation of a particular word form), we analyzed morphosyntactic predictability (the activation of morphological features of words) and its effect on reading times over and above lexical predictability. We found that for predicting reading times, cloze and corpus-based measures of both lexical and morphosyntactic predictability explained the same amount of variance. However, cloze and corpus-based lexical probabilities both independently contributed to a better model fit, whereas for morphosyntactic probabilities, the contributions of cloze and corpus-based measures were interchangeable. Therefore, morphosyntactic but not lexical corpus-based probabilities can substitute for cloze probabilities in reading experiments. Our results also indicate that in languages with rich inflectional morphology, such as Russian, when people engage in prediction, they are much more successful in predicting isolated morphosyntactic features than predicting the particular lexeme and its full morphosyntactic markup.

Added: Jan 29, 2021
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
Belaza A. M., Ryckebusch J., Schoors K. et al. Plos One. 2020. No. 15(10). P. e0240196.

Games involving virtual worlds are popular in several segments of the population and societies. The online environment facilitates that players from different countries interact in a common virtual world. Virtual worlds involving social and economic interactions are particularly useful to test social and economic theories. Using data from EVE Online, a massive online multi-player game simulating a fantasy galaxy, we analyse the relation between the real-world context in which players live and their in-game behaviour at the country level. We find that in-game aggressiveness to non-player characters is positively related to real-world levels of aggressiveness as measured by the Global Peace Index and the Global Terrorist Index at the country level. The opposite is true for in-game aggressiveness towards other players, which seems to work as a safety valve for real-world player aggressiveness. The ability to make in-game friends is also positively related to real-world levels of aggressiveness in much the same way. In-game trading behaviour is dependent on the macro-economic environment where players live. The unemployment rate and exchange rate make players trade more efficiently and cautiously in-game. Overall, we find evidence that the real-world environment affects in-game behaviour, suggesting that virtual worlds can be used to experiment and test social and economic theories, and to infer real-world behaviour at the country level.

Added: Oct 22, 2020
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
Uusküla A., Vickerman P., Raag M. et al. Plos One. 2020. Vol. 15. No. 10. P. e0240224.

Objective: We aim to show the feasibility of using an integrated prevention and care continuum (PCC) model as a complete and improved tool for HIV control measurement and programming. Alignment of prevention and care continua is essential to further improve health outcomes and minimize HIV transmission risk. Design: Cross-sectional study. Methods: Data from 977 persons who inject drugs (PWID) collected in 2011-2016 in Tallinn, Estonia, were used to construct an HIV PCC for PWID, stratified by risk for acquiring or transmitting HIV infection and by coverage of combined interventions. We also estimated the average protective effect of current levels of intervention provision.   Results: 74.4%, 20.3% and 35.2% of PWID were currently using needle and syringe programmes (NSP), drug treatment and HIV testing, respectively. 51.1% of current PWID were HIV seropositive and of those 62.5% were currently on antiretroviral therapy (ART) and 19.0% were virally suppressed. Across the PCC, individuals moved between categories of being aware and ever using drug treatment (resulting in -50% “leakage”); from ever having used to currently using drug treatment (-59%); between “ever testing” and “current (continuous) testing” (-62%); and from self-reported ART adherence to viral suppression (-70%). Use of prevention services was higher among those at risk of transmission (HIV positive). The overall reduction in acquisition risk among HIV-negative PWID was 77.7% (95% CrI 67.8-84.5%), estimated by the modelled protective effects of current levels of NSP, drug treatment and ART compared to none of these services. Conclusions: Our findings suggest that developing a cohesive model for HIV prevention and treatment is feasible and reflects the bi-directional relationships between prevention and care. The integrated continuum model indicates the major factors which may predict the epidemic course and control response.

Added: Oct 2, 2020
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
Farshchi M., Kiba A., Sawada T. Plos One. 2021. Vol. 16. No. 1: e0242581. P. 1-17.

Artists can represent a 3D object by using only contours in a 2D drawing. Prior studies have shown that people can use such drawings to perceive 3D shapes reliably, but it is not clear how useful this kind of contour information actually is in a real dynamical scene in which people interact with objects. To address this issue, we developed an Augmented Reality (AR) device that can show a participant a contour-drawing or a grayscale-image of a real dynamical scene in an immersive manner. We compared the performance of people in a variety of run-of-the-mill tasks with both contour-drawings and grayscale-images under natural viewing conditions in three behavioral experiments. The results of these experiments showed that the people could perform almost equally well with both types of images. This contour information may be sufficient to provide the basis for our visual system to obtain much of the 3D information needed for successful visuomotor interactions in our everyday life.

Added: Jan 23, 2021
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