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Regular version of the site
Of all publications in the section: 84
by name
by year
Kouyoumdjian F. G., Andreev E. M., Borschmann R. et al. Plos One. 2017. Vol. 12. No. 4. P. 1-11.


We aimed to explore whether mortality data are consistent with the view that aging is accelerated for people with a history of incarceration compared to the general population, using data on mortality rates and life expectancy for persons in Ontario, Canada. 


We obtained data from the Ontario Ministry of Community Safety and Correctional Services on all adults admitted to provincial correctional facilities in Ontario in 2000, and linked these data with death records from provincial vital statistics between January 1, 2000 and December 31, 2012. We used life table methods to calculate mortality rates and life expectancies for this cohort by sex and 5-year age group. We similarly generated population comparison rates using publicly available data for the general population of Ontario in 2006 as the midpoint of the follow up period. We compared these mortality indices between the 2000 Ontario prison cohort and the general population by age group and sex. 


The difference in all-cause mortality rates between the 2000 Ontario prison cohort and the general population was greatest for younger adults, with the prison cohort experiencing rates of death that would be expected for persons at least 15 years older at ages 20 to 44 for men and ages 20 to 59 for women. Life expectancy in the 2000 Ontario prison cohort was most similar to life expectancy of persons five years older in the general population at age intervals 20 to 45 in men and 20 to 30 in women. 


For most of adulthood, life expectancy and mortality rates are worse for adults with a history of incarceration than for the general population in Ontario, Canada. However, the association between mortality and incarceration status is modified by age, with the greatest relative burden of mortality experienced by younger persons with a history of incarceration and modified by sex, with worse relative mortality in women. Future research should explore the association between incarceration status and markers of aging including mortality, morbidity and physical appearance.

Added: Jun 7, 2017
Kirby K. R., Gray R. D., Greenhill S. J. et al. Plos One. 2016. Vol. 11. No. 7. P. e0158391.

From the foods we eat and the houses we construct, to our religious practices and political organization, to who we can marry and the types of games we teach our children, the diversity of cultural practices in the world is astounding. Yet, our ability to visualize and understand this diversity is limited by the ways it has been documented and shared: on a culture-by-culture basis, in locally-told stories or difficult-to-access repositories. In this paper we introduce D-PLACE, the Database of Places, Language, Culture, and Environment. This expandable and open-access database (accessible at https://d-place.org) brings together a dispersed corpus of information on the geography, language, culture, and environment of over 1400 human societies. We aim to enable researchers to investigate the extent to which patterns in cultural diversity are shaped by different forces, including shared history, demographics, migration/diffusion, cultural innovations, and environmental and ecological conditions. We detail how D-PLACE helps to overcome four common barriers to understanding these forces: i) location of relevant cultural data, (ii) linking data from distinct sources using diverse ethnonyms, (iii) variable time and place foci for data, and (iv) spatial and historical dependencies among cultural groups that present challenges for analysis. D-PLACE facilitates the visualisation of relationships among cultural groups and between people and their environments, with results downloadable as tables, on a map, or on a linguistic tree. We also describe how D-PLACE can be used for exploratory, predictive, and evolutionary analyses of cultural diversity by a range of users, from members of the worldwide public interested in contrasting their own cultural practices with those of other societies, to researchers using large-scale computational phylogenetic analyses to study cultural evolution. In summary, we hope that D-PLACE will enable new lines of investigation into the major drivers of cultural change and global patterns of cultural diversity.

Added: Sep 18, 2020
Keramati M., Gutkin B. Plos One. 2013. Vol. 8. No. 4.

Despite explicitly wanting to quit, long-term addicts find themselves powerless to resist drugs, despite knowing that drug-taking may be a harmful course of action. Such inconsistency between the explicit knowledge of negative consequences and the compulsive behavioral patterns represents a cognitive/behavioral conflict that is a central characteristic of addiction. Neurobiologically, differential cue-induced activity in distinct striatal subregions, as well as the dopamine connectivity spiraling from ventral striatal regions to the dorsal regions, play critical roles in compulsive drug seeking. However, the functional mechanism that integrates these neuropharmacological observations with the above-mentioned cognitive/behavioral conflict is unknown. Here we provide a formal computational explanation for the drug-induced cognitive inconsistency that is apparent in the addicts' “self-described mistake”. We show that addictive drugs gradually produce a motivational bias toward drug-seeking at low-level habitual decision processes, despite the low abstract cognitive valuation of this behavior. This pathology emerges within the hierarchical reinforcement learning framework when chronic exposure to the drug pharmacologically produces pathologicaly persistent phasic dopamine signals. Thereby the drug hijacks the dopaminergic spirals that cascade the reinforcement signals down the ventro-dorsal cortico-striatal hierarchy. Neurobiologically, our theory accounts for rapid development of drug cue-elicited dopamine efflux in the ventral striatum and a delayed response in the dorsal striatum. Our theory also shows how this response pattern depends critically on the dopamine spiraling circuitry. Behaviorally, our framework explains gradual insensitivity of drug-seeking to drug-associated punishments, the blocking phenomenon for drug outcomes, and the persistent preference for drugs over natural rewards by addicts. The model suggests testable predictions and beyond that, sets the stage for a view of addiction as a pathology of hierarchical decision-making processes. This view is complementary to the traditional interpretation of addiction as interaction between habitual and goal-directed decision systems.

Added: Mar 10, 2015
Jackson J. C., Van Egmond M., Choi V. K. et al. Plos One. 2019. Vol. 14. No. 9. P. e0221953.

Prejudiced attitudes and political nationalism vary widely around the world, but there has been little research on what predicts this variation. Here we examine the ecological and cultural factors underlying the worldwide distribution of prejudice. We suggest that cultures grow more prejudiced when they tighten cultural norms in response to destabilizing ecological threats. A set of seven archival analyses, surveys, and experiments (∑N = 3,986,402) find that nations, American states, and pre-industrial societies with tighter cultural norms show the most prejudice based on skin color, religion, nationality, and sexuality, and that tightness predicts why prejudice is often highest in areas of the world with histories of ecological threat. People's support for cultural tightness also mediates the link between perceived ecological threat and intentions to vote for nationalist politicians. Results replicate when controlling for economic development, inequality, conservatism, residential mobility, and shared cultural heritage. These findings offer a cultural evolutionary perspective on prejudice, with implications for immigration, intercultural conflict, and radicalization.

Added: Jul 24, 2020
Jackson J., van Egmond M., Choi V. et al. Plos One. 2019. P. 1-17.

Prejudiced attitudes and political nationalism vary widely around the world, but there has been little research on what predicts this variation. Here we examine the ecological and cultural factors underlying the worldwide distribution of prejudice. We suggest that cultures grow more prejudiced when they tighten cultural norms in response to destabilizing ecological threats. A set of seven archival analyses, surveys, and experiments (∑N = 3,986,402) find that nations, American states, and pre-industrial societies with tighter cultural norms show the most prejudice based on skin color, religion, nationality, and sexuality, and that tightness predicts why prejudice is often highest in areas of the world with histories of ecological threat. People’s support for cultural tightness also mediates the link between perceived ecological threat and intentions to vote for nationalist politicians. Results replicate when controlling for economic development, inequality, conservatism, residential mobility, and shared cultural heritage. These findings offer a cultural evolutionary perspective on prejudice, with implications for immigration, intercultural conflict, and radicalization

Added: Sep 23, 2019
Rykov Y., Koltsova O., Sinyavskaya Y. Plos One. 2020. Vol. 15. No. 4. P. 1-17.

The use of social network sites helps people to make and maintain social ties accumulating social capital, which is increasingly important for individual success. There is a wide variation in the amount and structure of online ties, and to some extent this variation is contingent on specific online user behaviors which are to date under-researched. In this work, we examine an entire city-bounded friendship network (N = 194,601) extracted from VK social network site to explore how specific online user behaviors are related to structural social capital in a network of geographically proximate ties. Social network analysis was used to evaluate individual social capital as a network asset, and multiple regression analysis–to determine and estimate the effects of online user behaviors on social capital. The analysis reveals that the graph is both clustered and highly centralized which suggests the presence of a hierarchical structure: a set of sub-communities united by city-level hubs. Against this background, membership in more online groups is positively associated with user’s brokerage in the location-bounded network. Additionally, the share of local friends, the number of received likes and the duration of SNS use are associated with social capital indicators. This contributes to the literature on the formation of online social capital, examined at the level of a large and geographically localized population.

Added: Jun 2, 2020
Kertesz-Farkas A., Juhász J., Szabó D. et al. Plos One. 2014. Vol. 9. No. 4.

Multispecies bacterial communities such as the microbiota of the gastrointestinal tract can be remarkably stable and resilient even though they consist of cells and species that compete for resources and also produce a large number of antimicrobial agents. Computational modeling suggests that horizontal transfer of resistance genes may greatly contribute to the formation of stable and diverse communities capable of protecting themselves with a battery of antimicrobial agents while preserving a varied metabolic repertoire of the constituent species. In other words horizontal transfer of resistance genes makes a community compatible in terms of exoproducts and capable to maintain a varied and mature metagenome. The same property may allow microbiota to protect a host organism, or if used as a microbial therapy, to purge pathogens and restore a protective environment.

Added: Nov 18, 2015
Hennig-Schmidt H., Lönnqvist J., Walkowitz G. Plos One. 2015. Vol. 10. No. 5. P. e0124622 .
Added: Oct 4, 2018
Bondarenko V., Gelfand M. S. Plos One. 2016. Vol. 11. No. 9. P. 1-16.

A typical eukaryotic gene is comprised of alternating stretches of regions, exons and introns, retained in and spliced out a mature mRNA, respectively. Although the length of introns may vary substantially among organisms, a large fraction of genes contains short introns in many species. Notably, some Ciliates (Paramecium and Nyctotherus) possess only ultra-short introns, around 25 bp long. In Paramecium, ultra-short introns with length divisible by three (3n) are under strong evolutionary pressure and have a high frequency of in-frame stop codons, which, in the case of intron retention, cause premature termination of mRNA translation and consequent degradation of the mis-spliced mRNA by the nonsense-mediated decay mechanism. Here, we analyzed introns in five genera of Ciliates, Paramecium, Tetrahymena, Ichthyophthirius, Oxytricha, and Stylonychia. Introns can be classified into two length classes in Tetrahymena and Ichthyophthirius (with means 48 bp, 69 bp, and 55 bp, 64 bp, respectively), but, surprisingly, comprise three distinct length classes in Oxytricha and Stylonychia (with means 33-35 bp, 47-51 bp, and 78-80 bp). In most ranges of the intron lengths, 3n introns are underrepresented and have a high frequency of in-frame stop codons in all studied species. Introns of Paramecium, Tetrahymena, and Ichthyophthirius are preferentially located at the 5' and 3' ends of genes, whereas introns of Oxytricha and Stylonychia are strongly skewed towards the 5' end. Analysis of evolutionary conservation shows that, in each studied genome, a significant fraction of intron positions is conserved between the orthologs, but intron lengths are not correlated between the species. In summary, our study provides a detailed characterization of introns in several genera of Ciliates and highlights some of their distinctive properties, which, together, indicate that splicing spellchecking is a universal and evolutionarily conserved process in the biogenesis of short introns in various representatives of Ciliates.

Added: Mar 13, 2017
Petrovskaya A., Kirillov B., Асмолова А. С. et al. Plos One. 2020. Vol. 15. No. 12. P. 1-15.

We aimed to replicate a published effect of transcranial direct-current stimulation (tDCS) -induced recognition enhancement over the human ventrolateral prefrontal cortex [1] and analyze the data with machine learning. We investigated effects over an adjacent region, the dorsolateral PFC. We found weak or absent effects over the VLPFC and DLPFC. We conducted machine learning studies to examine the effects of semantic and phonetic features on memorization, which revealed no effect of VLPFC tDCS on the original dataset or the current data. The highest contributing factor to memory performance was individual differences in memory not explained by word features, tDCS group, or sample size, while semantic, phonetic, and orthographic word characteristics did not contribute significantly. To our knowledge,We aimed to replicate a published effect of transcranial direct-current stimulation (tDCS) - induced recognition enhancement over the human ventrolateral prefrontal cortex (VLPFC) and analyze the data with machine learning. We investigated effects over an adjacent region, the dorsolateral prefrontal cortex (DLPFC). In total, we analyzed data from 97 participants after exclusions. We found weak or absent effects over the VLPFC and DLPFC. We conducted machine learning studies to examine the effects of semantic and phonetic features on memorization, which revealed no effect of VLPFC tDCS on the original dataset or the current data. The highest contributing factor to memory performance was individual differencesin memory not explained by word features, tDCS group, or sample size, while semantic, phonetic, and orthographic word characteristics did not contribute significantly. To our knowledge, this is the first tDCS study to investigate cognitive effects with machine learning, and future studies may benefit from studying physiological as well as cognitive effects with data-driven approaches and computational models.

Added: Dec 10, 2020
Kosonogov V., De Zorzi L., Honore J. et al. Plos One. 2017. Vol. 12. P. 1-15.

Functional infrared thermal imaging (fITI) is considered a promising method to measure emotional autonomic responses through facial cutaneous thermal variations. However, the facial thermal response to emotions still needs to be investigated within the framework of the dimensional approach to emotions. The main aim of this study was to assess how the facial thermal variations index the emotional arousal and valence dimensions of visual stimuli. Twenty-four participants were presented with three groups of standardized emotional pictures (unpleasant, neutral and pleasant) from the International Affective Picture System. Facial temperature was recorded at the nose tip, an important region of interest for facial thermal variations, and compared to electrodermal responses, a robust index of emotional arousal. Both types of responses were also compared to subjective ratings of pictures. An emotional arousal effect was found on the amplitude and latency of thermal responses and on the amplitude and frequency of electrodermal responses. The participants showed greater thermal and dermal responses to emotional than to neutral pictures with no difference between pleasant and unpleasant ones. Thermal responses correlated and the dermal ones tended to correlate with subjective ratings. Finally, in the emotional conditions compared to the neutral one, the frequency of simultaneous thermal and dermal responses increased while both thermal or dermal isolated responses decreased. Overall, this study brings convergent arguments to consider fITI as a promising method reflecting the arousal dimension of emotional stimulation and, consequently, as a credible alternative to the classical recording of electrodermal activity. The present research provides an original way to unveil autonomic implication in emotional processes and opens new perspectives to measure them in touchless conditions.

Added: Oct 1, 2019
Smirnov I., Thurner S. Plos One. 2017. Vol. 12. No. 8. P. 1-16.

Homophily, the tendency of individuals to associate with others who share similar traits, has been identified as a major driving force in the formation and evolution of social ties. In many cases, it is not clear if homophily is the result of a socialization process, where individuals change their traits according to the dominance of that trait in their local social networks, or if it results from a selection process, in which individuals reshape their social networks so that their traits match those in the new environment. Here we demonstrate the detailed temporal formation of strong homophily in academic achievements of high school and university students. We analyze a unique dataset that contains information about the detailed time evolution of a friendship network of 6,000 students across 42 months. Combining the evolving social network data with the time series of the academic performance (GPA) of individual students, we show that academic homophily is a result of selection: students prefer to gradually reorganize their social networks according to their performance levels, rather than adapting their performance to the level of their local group. We find no signs for a pull effect, where a social environment of good performers motivates bad students to improve their performance. We are able to understand the underlying dynamics of grades and networks with a simple model. The lack of a social pull effect in classical educational settings could have important implications for the understanding of the observed persistence of segregation, inequality and social immobility in societies.

Added: Aug 31, 2017
Babkina T., Menshikov I., Shklover A. et al. Plos One. 2017. Vol. 12. No. 11. P. 1-17.

In this research, the social behavior of the participants in a Prisoner's Dilemma laboratory game is explained on the basis of the quantal response equilibrium concept and the representation of the game in Markov strategies. In previous research, we demonstrated that social interaction during the experiment has a positive influence on cooperation, trust, and gratefulness. This research shows that the quantal response equilibrium concept agrees only with the results of experiments on cooperation in Prisoner’s Dilemma prior to social interaction. However, quantal response equilibrium does not explain of participants’ behavior after social interaction. As an alternative theoretical approach, an examination was conducted of iterated Prisoner's Dilemma game in Markov strategies. We built a totally mixed Nash equilibrium in this game; the equilibrium agrees with the results of the experiments both before and after social interaction.

Added: Jun 4, 2018
Brederoo S., Bos L., Dragoy O. et al. Plos One. 2015. Vol. 10. No. 4.

Verbs and other temporal expressions allow speakers to specify the location of events in time, as well as to move back and forth in time, shifting in a narrative between past, present and future. The referential flexibility of temporal expressions is well understood in linguistics but its neurocognitive bases remain unknown. Here we aimed to obtain a neural signature of time shifting in natural language. We analyzed event-related potentials (ERPs) and oscillatory responses to occurrences of the word ‘now’ and of verbs in Punctual (‘An hour ago the boy stole a candy and now he peeled the fruit’) and Iterative (‘The entire afternoon the boy stole candy and now he peeled the fruit’) contexts. ‘An hour ago’ introduces a time frame that lies entirely in the past, ‘now’ shifts the narrative to the present, and ‘peeled’ shifts it back to the past. These two time shifts in Punctual contexts are expected to leave very similar traces on electrophysiological responses. ‘The entire afternoon’ may encompass past and present: both ‘now’ and ‘peeled’ are consistent with that time frame, therefore no time shift is required. We found no difference in ERPs between Punctual and Iterative contexts either at ‘now’ or at the verb. However, time shifts modulated brain oscillations. ‘Now’ and ‘peeled’ in Punctual contexts resulted in nearly identical signals: an increase in gamma power with a left-anterior distribution. Gamma bursts were absent in Iterative contexts. We propose that gamma oscillations here reflect operations that bind temporal variables to the values allowed by the constraints introduced by temporal expressions in discourse.

Added: Dec 15, 2014
Cugmas M., Ferligoj A., ŽIBERNA A. Plos One. 2018. Vol. 13. No. 5. P. 1-24.

This paper addresses the question of whether one can generate networks with a given global structure (defined by selected blockmodels, i.e., cohesive, core-periphery, hierarchical, and transitivity), considering only different types of triads. Two methods are used to generate networks: (i) the newly proposed method of relocating links; and (ii) the Monte Carlo Multi Chain algorithm implemented in the ergm package in R. Most of the selected blockmodel types can be generated by considering all types of triads. The selection of only a subset of triads can improve the generated networks’ blockmodel structure. Yet, in the case of a hierarchical blockmodel without complete blocks on the diagonal, additional local structures are needed to achieve the desired global structure of generated networks. This shows that blockmodels can emerge based only on local processes that do not take attributes into account.

Added: Nov 2, 2018
Dybo A., Kushniarevich A., Utevska O. et al. Plos One. 2015. Vol. 10. No. 9.

The Slavic branch of the Balto-Slavic sub-family of Indo-European languages underwent rapid divergence as a result of the spatial expansion of its speakers from Central-East Europe, in early medieval times. This expansion-mainly to East Europe and the northern Balkans-resulted in the incorporation of genetic components from numerous autochthonous populations into the Slavic gene pools. Here, we characterize genetic variation in all extant ethnic groups speaking Balto-Slavic languages by analyzing mitochondrial DNA (n = 6,876), Y-chromosomes (n = 6,079) and genome-wide SNP profiles (n = 296), within the context of other European populations. We also reassess the phylogeny of Slavic languages within the Balto-Slavic branch of Indo-European. We find that genetic distances among Balto-Slavic populations, based on autosomal and Y-chromosomal loci, show a high correlation (0.9) both with each other and with geography, but a slightly lower correlation (0.7) with mitochondrial DNA and linguistic affiliation. The data suggest that genetic diversity of the present-day Slavs was predominantly shaped in situ, and we detect two different substrata: 'central-east European' for West and East Slavs, and 'south-east European' for South Slavs. A pattern of distribution of segments identical by descent between groups of East-West and South Slavs suggests shared ancestry or a modest gene flow between those two groups, which might derive from the historic spread of Slavic people.

Added: Nov 14, 2019
Kessenikh A., Gnuchikh E., Bazhenov S. et al. Plos One. 2020. Vol. 15. No. 8.

The toxic effect of strained hydrocarbon 2,2'—bis (bicyclo[2.2.1]heptane) (BBH) was studied using whole-cell bacterial lux-biosensors based on Escherichia coli cells in which luciferase genes are transcriptionally fused with stress-inducible promoters. It was shown that BBH has the genotoxic effect causing bacterial SOS response however no alkylating effect has been revealed. In addition to DNA damage, there is an oxidative effect causing the response of OxyR/S and SoxR/S regulons. The most sensitive to BBH lux-biosensor was E. coli pSoxS-lux which reacts to the appearance of superoxide anion radicals in the cell. It is assumed that the oxidation of BBH leads to the generation of reactive oxygen species, which provide the main contribution to the genotoxicity of this substance

Added: Mar 2, 2021
Мальков Ю. А., Ponomarenko A. Plos One. 2016. Vol. 11. No. 6. P. 1-14.

Navigability, an ability to find a logarithmically short path between elements using only local information, is one of the most fascinating properties of real-life networks. However, the exact mechanism responsible for the formation of navigation properties remained unknown. We show that navigability can be achieved by using only two ingredients present in the majority of networks: network growth and local homophily, giving a persuasive answer how the navigation appears in real-life networks. A very simple algorithm produces hierarchical self-similar optimally wired navigable small world networks with exponential degree distribution by using only local information. Adding preferential attachment produces a scale-free network which has shorter greedy paths, but worse (power law) scaling of the information extraction locality (algorithmic complexity of a search). Introducing saturation of the preferential attachment leads to truncated scale-free degree distribution that offers a good tradeoff between these parameters and can be useful for practical applications. Several features of the model are observed in real-life networks, in particular in the brain neural networks, supporting the earlier suggestions that they are navigable.

Added: Sep 9, 2016
Thomas G., Poortinga W., Sautkina E. Plos One. 2016. Vol. 11. No. 4. P. 1-16.

Repeated behaviours in stable contexts can become automatic habits. Habits are resistant to information-based techniques to change behaviour, but are contextually cued, so a change in behaviour context (e.g., location) weakens habit strength and can facilitate greater consideration of the behaviour. This idea was demonstrated in previous work, whereby people with strong environmental attitudes have lower car use, but only after recently moving home. We examine the habit discontinuity hypothesis by analysing the Understanding Society dataset with 18,053 individuals representative of the UK population, measuring time since moving home, travel mode to work, and strength of environmental attitudes. Results support previous findings where car use is significantly lower among those with stronger environmental views (but only after recently moving home), and in addition, demonstrate a trend where this effects decays as the time since moving home increases. We discuss results in light of moving into a new home being a potential ‘window of opportunity’ to promote pro-environmental behaviours.

Added: Oct 3, 2018
Oksuzyan A., Demakakos P., Shkolnikova M. A. et al. Plos One. 2017. Vol. 12. No. 9. P. 1-16.


This study compares handgrip strength and its association with mortality across studies conducted in Moscow, Denmark, and England.


The data collected by the Study of Stress, Aging, and Health in Russia, the Study of Middle-Aged Danish Twins and the Longitudinal Study of Aging Danish Twins, and the English Longitudinal Study of Ageing was utilized.


Among the male participants, the age-standardized grip strength was 2 kg and 1 kg lower in Russia than in Denmark and in England, respectively. The age-standardized grip strength among the female participants was 1.9 kg and 1.6 kg lower in Russia than in Denmark and in England, respectively. In Moscow, a one-kilogram increase in grip strength was associated with a 4% (hazard ratio [HR] = 0.96, 95% confidence interval [CI]: 0.94, 0.99) reduction in mortality among men and a 10% (HR = 0.90, 95%CI: 0.86, 0.94) among women. Meanwhile, a one-kilogram increase in grip strength was associated with a 6% (HR = 0.94, 95%CI: 0.93, 0.95) and an 8% (HR = 0.92, 95%CI: 0.90, 0.94) decrease in mortality among Danish men and women, respectively, and with a 2% (HR = 0.98, 95%CI: 0.97, 0.99) and a 3% (HR = 0.97, 95%CI: 0.95, 0.98) reduction in mortality among the English men and women, respectively.


The study suggests that, although absolute grip strength values appear to vary across the Muscovite, Danish, and English samples, the degree to which grip strength is predictive of mortality is comparable across national populations with diverse socioeconomic and health profiles and life expectancy levels.

Added: Oct 25, 2017
Tomkins S., Collier T., Oralov A. et al. Plos One. 2012. Vol. 7. No. 2.
Added: Jun 21, 2017