Contents Authors................................................................................................................................ 7 Acknowledgements............................................................................................................9 Executive summary ........................................................................................................... 11 1. Introduction....................................................................................................................13 Riccardo Valentini, Pekka Leskinen, Pieter Johannes Verkerk, Gert-Jan Nabuurs, George Safonov and Elena Kulikova 2. State of Russian forests and forestry............................................................................17 Dmitry Zamolodchikov, Anatoly Shvidenko, Sergey Bartalev, Elena Kulikova, Alexander Held, Riccardo Valentini and Marcus Lindner 2.1 Major characteristics of Russian forests..........................................................17 2.2 Natural forest disturbances.............................................................................. 21 2.3 Forest governance and use..............................................................................26 2.4 Ecosystem functions and services of Russia’s forests....................................28 2.5 Key challenges in forest resource management..............................................35 2.6 Key messages.................................................................................................... 38 3. Climate change in Russia – past, present and future................................................. 45 Riccardo Valentini, Dmitry Zamolodchikov, Christopher Reyer, Sergio Noce, Monia Santini and Marcus Lindner 3.1 Observed changes of Russian climate in recent decades.............................. 45 3.2 Climate change scenarios................................................................................48 3.3 Key messages.....................................................................................................51 4. Climate change and Russian forests: impacts, vulnerability and adaptation needs... 53 Christopher Reyer, Marcus Lindner, Dmitry Zamolodchikov, Anatoly Shvidenko, Martin Gutsch and Sergey Bartalev 4.1 Observed impacts of climate change...............................................................53 4.2 Projected impacts.............................................................................................56 4.3 Vulnerability assessment................................................................................. 61 4.4 Adaptation needs............................................................................................. 64 4.5 Key messages....................................................................................................67

5. Climate-Smart Forestry in Russia and potential climate change mitigation benefits.............................................................................................................................. 73 Bas Lerink, Mariana Hassegawa, Alexander Kryshen, Anton Kovalev, Eldar Kurbanov, Gert-Jan Nabuurs, Sergei Moshnikov and Pieter Johannes Verkerk 5.1 Introduction...................................................................................................... 73 5.2 Approach and general scenario assumptions.................................................74 5.3 Case study: Republic of Karelia.......................................................................78 5.4 Case study: Republic of Mari El.......................................................................84 5.5 Case study: Angara macro-district (Krasnoyarsk kray).................................. 91 5.6 Concluding remarks, discussion and implications....................................... 98 5.7 Key messages...................................................................................................101 6. The role of the bioeconomy in climate change mitigation in Russia..................... 105 Pekka Leskinen, Jo Van Brusselen, Mariana Hassegawa, Alexander Alekseev, Natalia Lukina, Olga Rakitova, George Safonov, Elena Kulikova and Mikhail Safonov 6.1 Introduction.................................................................................................... 105 6.2 The bioeconomy concept in Russia...............................................................106 6.3 The link between bioeconomy and climate change mitigation.................. 107 6.4 State of Russian forest industry and potential for bioeconomy................... 111 6.5 Sectoral development and outlook................................................................. 113 6.6 Summary and conclusions: Opportunities and challenges for a bioeconomy in Russia.....................................................................................123 6.7 Key messages...................................................................................................125 7. Conclusions.................................................................................................................. 131 Pekka Leskinen, Jo Van Brusselen, Marcus Lindner, Gert-Jan Nabuurs, Pieter Johannes Verkerk, Natalia Lukina, Sergey Bartalev and Elena Kulikova 7.1 Forest resources............................................................................................... 131 7.2 Climate change impacts, adaptation and mitigation....................................132 7.3 Forest management........................................................................................ 133 7.4 Enabling environment for a bioeconomy......................................................134 7.5 Holistic view.................................................................................................... 135 7.6 Key messages and next steps ........................................................................ 136

Forest ecosystems, their products and services play an important role in achieving ambitious climate change mitigation objectives at the same time requiring profound adaptation to climate change. Forest management schemes to support climate action have to be developed within their regional context but also have to be aligned with national or EU-level climate, forest and sustainability policies. The conference on “Managing forests in the 21st century” is the final conference of the FORMASAM, REFORCE and FOREXCLIM research projects. The conference bringstogether scientific experts on forest management from all over Europe facing very specific management challenges. The aim isto discuss and improve the understanding the role of forests and forest management in the context of climate change. The conference addresses climate change impacts, as well as needs for mitigation and adaptation especially with regard to the following scientific questions: 1. What are the impacts of climate extremes and disturbances? 2. What are the management challenges (and options) for resilient forests? 3. What can we do to increase the contribution of forest management to climate change mitigation?

This is the third book in a series on Medieval Novgorod and its surroundings and deals with a substantial body of animal bones that have been recovered over the last decade. The zooarchaeological evidence is discussed by the editor and a number of English and Russian specialists who dug the site, looking at domestic exploitation of animals, diet, animal husbandry, and butchery practices. Detailed data sets are provided to enable the reader to make comparisons with their own research, but the book is also suitable for those with a more general interest in Medieval Russian archaeology.

Cancer cells require exogenous methionine for survival and therefore methionine restriction is a promising avenue for treatment. The basis for methionine dependence in cancer cells is still not entirely clear. While the lack of the methionine salvage enzyme methylthioadenosine phosphorylase (MTAP) is associated with methionine auxotrophy in cancer cells, there are other causes for tumors to require exogenous methionine. Restricting methionine by diet or by enzyme depletion, alone or in combination with certain chemotherapeutics, is a promising antitumor strategy.

This book examines how Russia, the world’s most complicated country, is governed. As it resumes its place at the centre of global affairs, the book explores Russia’s overarching strategies, and how it organizes itself (or not) in policy areas ranging from foreign policy and national security to health care, education, immigration, science, sport, agriculture, the environment and criminal justice. The book also discusses the structures and institutions on which Russia relies in order to deliver its goals in these areas of national life, as well as what’s to be done, in policy terms, to improve the country’s performance in its first post-Soviet century. Edited by Irvin Studin, the book includes contributions from a tremendous list of Russia’s leading thinkers and specialists, including Alexei Kudrin, Vladimir Mau, Alexander Auzan, Simon Kordonsky, Fyodor Lukyanov, Natalia Zubarevich and Andrey Melville.

The development and use of Genetically modified organisms (GMOs) has been a contentios subject for the last three decades. while there has been a number of social science analysis of the issues, this is the first book to assess the role of non-governmental organizations (NGOs) in the debate at such wide geographic scale. The various posiotions, for and against GMOs, particularly with regards to trangenic crops, articulated by NGOs in the debate are dissected, classified and juxtaposed to corresponding campaigns. these are discussed in the context of paradigms, including nature fundamentalism and the organic movement, post-colonialism, food sovereignty, anti-globalism, sustainability and feminism. This book also analyses how NGOs interprete the debate and the persuasive communication tactics. 

 

The Paris Climate Agreement established a new target of combating global warming "well below 2 degrees Celsius". This goal will lead to the transformation and deep decarbonization of world economy aiming at nearly zero carbon emissions soon after 2050. The Northeastern Asian countries (responsible for 40% of global CO2 emissions) have all rechnological, resource and ivnestment potential for decarbonization both domestically and internationally, and can show leadership in this efforts on global scale.

The book provides the first in-depth, multidisciplinary study of reurbanization in Russia's Arctic regions, with a specific focus on new mobility patterns, and the resulting birth of new urban Arctic identities in which newcomers and labor migrants form a rising part. It is an invaluable reference for all those interested in current trends in circumpolar regions, showing how the Arctic is becoming more diverse culturally, but also more integrated into globalized trends in terms of economic development, urban sustainability, and migration.

The piblication provides the key lessons learnt from DDPP project experience on designing long-term pathways of low carbon development for 16 world largest economies. The Paris Climate Agreement requires countries to build their concrete vision of the national low-emission transition, consistent with global climate goals that would widely shared by domestic stakeholders and explicitly articulated with domestic socio-economic priorities. We analyze the experience of USA, France, Germany, Russia, China, India, Indonesia, Japan, UK, Mexico, Canada, Italy, Brazil in projecting the deep decarbonization scenarios for their economies by 2050.

The book presents a brief summary of the scientific research on deep decarbonization of 16 largest economies by 2050.

This report examines the changes happening in Russia ever since the issue of global warming was introduced on the global agenda. Only today, after the planet has experienced a variety of catastrophic natural disasters, have world leaders and decision makers grown more aware of the urgency of the problem. In Russia, where climate changes have been more significant than globally on average, the government has increased its objectives in reducing greenhouse gas emissions and put forward a number of initiatives and green policy measures to achieve more sustainability in the long term. Russia’s target for greenhouse gas emissions in 2030 is set at 70-75 percent of the base level of 1990, according to the new action plan adopted by the Kremlin. Other states also recognize the problem but their positions differ in the way the issue should be solved. India, China, the U.S. and Brazil, all of which are important players analyzed in the report, find it hard to reach common ground in reaching a globally binding agreement. Whether this will be done ultimately depends on the outcome of the Paris climate change conference. The report also considers the state of the Russian climate change movement from the experience of NGO activities in Russia, provides an overview of the development of the Russian green energy sector with specific success stories and analyzes the prospects of renewable energy development in different regions of the country.

This supplementary material contains case studies presenting specific aspects of the DDPP country pathways. They illustrate and complement the cross-cutting analysis included in the 2015 DDPP synthesis report

The Deep Decarbonization Pathways Project (DDPP) is a collaborative global research initiative seeking to understand how individual countries can transition, on a technological, socio-economic and policy “pathway”, to a low-carbon economy consistent with the internationally agreed goal of limiting anthropogenic warming to less than 2 degrees Celsius (2°C). Achieving this goal requires that the world cut global net emissions of greenhouse gases (GHG) so that they approach zero between 2050 and 2075, consistent with the Intergovernmental Panel on Climate Change (IPCC)1 2014 findings that to ensure a better-than-even chance of remaining below a 2°C temperature rise, global annual emissions will need to be reduced 42%–57% by 2050 (relative to 2010), and 73%–107% by 2100. This will entail, more than any other factor, the profound transformation of energy systems through steeply reducing carbon intensity in all sectors of the economy. We call this transition “deep decarbonization” and our products, Deep Decarbonization Pathways (DDPs).

The present volume is the fourth issue of the Yearbook series entitled ‘Evolution’. The title of the present volume is ‘From Big Bang to Nanorobots’. In this way we demonstrate that all phases of evolution and Big History are covered in the articles of the present Yearbook. Several articles also present the forecasts about future development.

The main objective of our Yearbook as well as of the previous issues is the creation of a unified interdisciplinary field of research in which the scientists specializing in different disciplines could work within the framework of unified or similar paradigms, using the common terminology and searching for common rules, tendencies and regularities. At the same time for the formation of such an integrated field one should use all available opportunities: theories, laws and methods. In the present volume, a number of such approaches are used.

The volume consists of four sections: Universal Evolutionary Principles; Biosocial Evolution, Ecological Aspects, and Consciousness; Projects for the Future; In Memoriam.

This Yearbook will be useful both for those who study interdisciplinary macroproblems and for specialists working in focused directions, as well as for those who are interested in evolutionary issues of Cosmology, Biology, History, Anthropology, Economics and other areas of study. More than that, this edition will challenge and excite your vision of your own life and the new discoveries going on around us!

The Deep Decarbonization Pathways Project (DDPP) is a collaborative initiative to understand and show how individual countries can transition to a low-carbon economy and how the world can meet the internationally agreed target of limiting the increase in global mean surface temperature to less than 2 degrees Celsius (°C). Achieving the 2°C limit will require that global net emissions of greenhouse gases (GHG) approach zero by the second half of the century. This will require a profound transformation of energy systems by mid-century through steep declines in carbon intensity in all sectors of the economy, a transition we call “deep decarbonization.” Successfully transitioning to a low-carbon economy will require unprecedented global cooperation, including a global cooperative effort to accelerate the development and diffusion of some key low carbon technologies.

This collection is a special issue of Russian Sociological Review dedicated to the concept of border. The concept itself seems to draw attention in many disciplines. As spatial phenomena, borders are always drawn in spaces, while social scientists, philosophers and other academics often have different meanings of space. Recent reconsiderations of space in terms of networks, flows and events, bring even more complexity to the concept. The current volume contributes to both theoretical and empirical studies of borders on various levels. Contributions look at the relevant phenomena from contemporary or historical perspectives, study narratives about borders, reconstructions of the empirical configurations of borders and other objects (such as bodies), exploring how borders emerge and reshape existing spaces, etc. Overall, the issue contributes to the emerging interdisciplinary field of border studies and encourages cross-disciplinary dialogue.

 

Work-book «The current state of the Russian oil and gas industry» is offered for publication as a training aid for students qualified at the direction 131000 “Oil and gas engineering”. We have described the geology of hydrocarbons, in particular - the geology of heavy oil, unconventional resources of energy, etc. In this workbook there are also methods for the development of deposits of heavy oil and produce shale oil. Special attention was given to unconventional sources of hydrocarbons, exactly, gas hydrates and clayey shale. Novelty of work-book is presentation of oil and gas terminology to students from China. This work-book is published for the first time and will be very useful for self-study students of oil and gas disciplines, as well as oil and gas terms in Russian, English and Chinese. The manuscript is classified as «Approved by UMO on Higher Education in the field of applied geology as a work book for students enrolled in the direction 131000 “Oil and Gas Engineering”».

Handedness is the most prominent trait of functional asymmetry in humans, associated with lateralized cognitive functions and considered in relation to mental disorders. However, the neuroanatomical correlates of handedness are still unclear. It has been hypothesized that the structural properties of sub-regions of the corpus callosum (CC) are linked to handedness. Nevertheless, tractography studies of the relation between directly measured structural properties of CC subregions and handedness are lacking. The Constrained Spherical Deconvolution (CSD) approach enables full reconstruction of the sub-regions of the CC. The current study aimed to investigate the relation between the structural properties of the CC, such as volume and the CSD metric, referred to as hindrance modulated orientational anisotropy (HMOA), and handedness. Handedness was considered in two dimensions: direction (right-handed, ambidextrous, left-handed) and degree (the absolute values of Handedness quotient). We found no association between 1) volume or HMOA as a proxy of microstructural properties, namely the axonal diameter and fiber dispersion, of each sub-region and 2) either the direction or the degree of handedness. These findings suggest the absence of a direct relation between sub-regions of the CC and handedness, demonstrating the necessity of future tractography studies.

This paper presents a novel rodent avoidance test. We have developed a specialized device and procedures that expand the possibilities for exploration of the processes of learning and memory in a psychophysiological experiment. The device consists of a current stimulating electrode-platform and custom software that allows to control and record real-time experimental protocols as well as reconstructs animal movement paths. The device can be used to carry out typical footshock-avoidance tests, such as passive, active, modified active and pedal-press avoidance tasks. It can also be utilized in the studies of prosocial behavior, including cooperation, competition, emotional contagion and empathy. This novel footshock-avoidance test procedure allows flexible currentstimulating settings. In our work, we have used slow-rising current. A test animal can choose between the current rise and time-out intervals as a signal for action in footshock avoidable tasks. This represents a choice between escape and avoidance. This method can be used to explore individual differences in decisionmaking and choice of avoidance strategies. It has been shown previously that a behavioral act, for example, pedal-pressing is ensured by motivation-dependent brain activity (avoidance or approach). We have created an experimental design based on tasks of instrumental learning: pedal-pressing in an operant box results in a reward, which is either a piece of food in a feeder (food-acquisition behavior) or an escape-platform (footshock-avoidance behavior). Data recording and analysis were performed using custom software, the open source Accord.NET Framework was used for real-time object detection and tracking.

Body size is correlated with many critical behavioral and developmental patterns in carnivores, including domestic dogs. The body masses and bite forces of archaeological dog remains from Siberia and the Russian Far East were estimated to make inferences regarding their behaviors and capacitis. The dogs date from ~10,000–100 cal. BP and derive from archaeological sites spanning from steppe environments in the south to tundra regions of the northern Arctic. The dogs exhibit a four-fold difference in body mass, ranging from 7.6 to 32.5 kg, but have a mean body mass of only 16.4 kg. Bite forces are around only half those of modern wolves, indicating that the dogs had greatly reduced abilities to grasp and masticate prey and food items. The dogs exhibit a slight decrease in body size through time, perhaps due to human selection or greater survival rates for smaller individuals in human-dominated food environments. Dog body size variance within individual archaeological sites was as high as in a sample of modern wolves from throughout the study area, suggesting little strict human control over body size. No correlation was found between body size and site latitude, suggesting that Bergmann’s rule does not hold for these canids. Human shelters may provide a buffer against low temperatures that might favour larger body sizes at high latitudes. About 90% of the analyzed dogs have estimated body masses less than 21.5 kg, suggesting most were best adapted for procuring prey smaller than themselves—the dogs were not capable of taking down larger prey without the assistance of humans. Estimated dog body masses cannot eliminate the possibility that many of the animals were used for pulling sleds, and nearly all were capable of packing modest loads on their backs. Livestock guarding dogs are not well-evidenced by the body mass data, but herding dogs are a possibility in all of the pastoral or agricultural settings analyzed

Sialidases, or neuraminidases, are involved in several human disorders such as neurodegenerative, infectious and cardiovascular diseases, and cancers. Accumulative data have shown that inhibition of neuraminidases, such as NEU1 sialidase, may be a promising pharmacological target, and selective inhibitors of NEU1 are therefore needed to better understand the biological functions of this sialidase. In the present study, we designed interfering peptides (IntPep) that target a transmembrane dimerization interface previously identified in human NEU1 that controls its membrane dimerization and sialidase activity. Two complementary strategies were used to deliver the IntPep into cells, either flanked to a TAT sequence or non-tagged for solubilization in detergent micelles. Combined with molecular dynamics simulations and heteronuclear NMR studies in membrane-mimicking environments, our results show that these IntPep are able to interact with the dimerization interface of human NEU1, to disrupt membrane NEU1 dimerization and to strongly decrease its sialidase activity at the plasma membrane. In conclusion, we report here new selective inhibitors of human NEU1 of strong interest to elucidate the biological functions of this sialidase.

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.

Animals living in extremely high elevations have to adapt to low temperatures and low oxygen availability (hypoxia), but the underlying genetic mechanisms associated with these adaptations are still unclear. The mitochondrial respiratory chain can provide over 95% of the ATP in animal cells, and its efficiency is influenced by temperature and oxygen availability. Therefore, the respiratory chain complexes could be important molecular targets for positive selection associated with respiratory adaptation in high altitude environments. Here, we investigated positive selection in five respiratory chain complexes and their assembly factors by analyzing sequences of 106 genes obtained through RNA-seq of all 15 Chinese Phrynocephalus lizard species, which are distributed from lowlands to the Tibetan plateau (average elevation above 4500m). Our results indicate that evidence of positive selection on respiratory chain complex genes is not significantly different from assembly factors, and we found no difference in selective pressures among the five complexes. We specifically looked for positive selection in lineages where changes in habitat elevation happened. The group of lineages evolving from low to high altitude show stronger signals of positive selection than lineages evolving from high to low elevations. Lineages evolving from low to high elevation also have more shared codons under positive selection, though the changes are not equivalent at the amino acid level. This study advances our understanding of the genetic basis of animal respiratory metabolism evolution in extreme high environments, and provides candidate genes for further confirmation with functional analyses.

Background: Biological networks are representative of the diverse molecular interactions that occur within cells. Some of the commonly studied biological networks are modeled through protein-protein interactions, gene regulatory, and metabolic pathways. Among these, metabolic networks are probably the most studied, as they directly influence all physiological processes. Exploration of biochemical pathways using multigraph representation is important in understanding complex regulatory mechanisms. Feature extraction and clustering of these networks enable grouping of samples obtained from different biological specimens. Clustering techniques separate networks depending on their mutual similarity. Results: We present a clustering analysis on tissue-specific metabolic networks for single samples from three primary tumor sites: breast, lung, and kidney cancer. The metabolic networks were obtained by integrating genome scale metabolic models with gene expression data. We performed network simplification to reduce the computational time needed for the computation of network distances. We empirically proved that networks clustering can characterize groups of patients in multiple conditions. Conclusions: We provide a computational methodology to explore and characterize the metabolic landscape of tumors, thus providing a general methodology to integrate analytic metabolic models with gene expression data. This method represents a first attempt in clustering large scale metabolic networks. Moreover, this approach gives the possibility to get valuable information on what are the effects of different conditions on the overall metabolism.

Long-term (2009–2019) field studies of the CO2 fluxes over the Valday upland in north-western European Russia were performed in an old-growth spruce-dominated forest subject to the combined effects of climate change, bark beetle attacks and windfall events. The annual carbon uptake within the study area decreased from − 300 g C m−2 yr−1 in 2010–2011 to − 95 g C m−2 yr−1 in 2018 as a result of progressive tree mortality. However, mortality did not cause a significant reduction in specific ecosystem respiration. The respiration of the damaged forest was formed by efflux from soil (64.8%), living vegetation (15.5%), hotspots under dry standing trees (12.1%) and decomposition of woody debris (7.6%). High correlations between net ecosystem exchange and dry standing spruce stocks and average soil CO2 efflux were found. The decrease in the carbon sink was followed by a decline in evapotranspiration from 0.0142 ± 0.0003 g H2O m−2 s−1 for May–October 2010 to 0.0116 ± 0.0002 g H2O m−2 s−1 in 2018. We assumed that the decrease in carbon uptake was due to both the reduction in primary tree production and the decrease in the area of the unaffected stands. Our estimates show that an increase in tree mortality up to 27% of a stand area could turn an old-growth spruce forest into a net source of CO2. This should be taken into account when considering human-induced and climate-related effects on boreal forests.

Recent years have witnessed a massive push towards reproducible research in neuroscience. Unfortunately, this endeavor is often challenged by the large diversity of tools used, project-specific custom code and the difficulty to track all user-defined parameters. NeuroPycon is an open-source multi-modal brain data analysis toolkit which provides Python-based template pipelines for advanced multi-processing of MEG, EEG, functional and anatomical MRI data, with a focus on connectivity and graph theoretical analyses. Importantly, it provides shareable parameter files to facilitate replication of all analysis steps. NeuroPycon is based on the NiPype framework which facilitates data analyses by wrapping many commonly-used neuroimaging software tools into a common Python environment. In other words, rather than being a brain imaging software with is own implementation of standard algorithms for brain signal processing, NeuroPycon seamlessly integrates existing packages (coded in python, Matlab or other languages) into a unified python framework. Importantly, thanks to the multi-threaded processing and computational efficiency afforded by NiPype, NeuroPycon provides an easy option for fast parallel processing, which critical when handling large sets of multi-dimensional brain data. Moreover, its flexible design allows users to easily configure analysis pipelines by connecting distinct nodes to each other. Each node can be a Python-wrapped module, a user-defined function or a well-established tool (e.g. MNE-Python for MEG analysis, Radatools for graph theoretical metrics, etc.). Last but not least, the ability to use NeuroPycon parameter files to fully describe any pipeline is an important feature for reproducibility, as they can be shared and used for easy replication by others. The current implementation of NeuroPycon contains two complementary packages: The first, called ephypype, includes pipelines for electrophysiology analysis and a command-line interface for on the fly pipeline creation. Current implementations allow for MEG/EEG data import, pre-processing and cleaning by automatic removal of ocular and cardiac artefacts, in addition to sensor or source-level connectivity analyses. The second package, called graphpype, is designed to investigate functional connectivity via a wide range of graph-theoretical metrics, including modular partitions. The present article describes the philosophy, architecture, and functionalities of the toolkit and provides illustrative examples through interactive notebooks. NeuroPycon is available for download via github (https://github.com/neuropycon) and the two principal packages are documented online (https://neuropycon.github.io/ephypype/index.html, and https://neuropycon.github.io/graphpype/index.html). Future developments include fusion of multi-modal data (eg. MEG and fMRI or intracranial EEG and fMRI). We hope that the release of NeuroPycon will attract many users and new contributors, and facilitate the efforts of our community towards open source tool sharing and development, as well as scientific reproducibility.

Adaptive introgression - the flow of adaptive genetic variation between species or populations - has attracted significant interest in recent years and it has been implicated in a number of cases of adaptation, from pesticide resistance and immunity, to local adaptation. Despite this, methods for identification of adaptive introgression from population genomic data are lacking. Here, we present Ancestry_HMM-S, a Hidden Markov Model based method for identifying genes undergoing adaptive introgression and quantifying the strength of selection acting on them. Through extensive validation, we show that this method performs well on moderately sized datasets for realistic population and selection parameters. We apply Ancestry_HMM-S to a dataset of an admixed Drosophila melanogaster population from South Africa and we identify 18 loci which show signatures of adaptive introgression, four of which have previously been shown to confer resistance to insecticides. Ancestry_HMM-S provides a powerful method for inferring adaptive introgression in datasets that are typically collected when studying admixed populations. This method will enable powerful insights into the genetic consequences of admixture across diverse populations. Ancestry_HMM-S can be downloaded from https://github.com/jesvedberg/Ancestry_HMM-S/.

The ongoing pandemic of SARS-CoV-2 presents novel challenges and opportunities for the use of phylogenetics to understand and control its spread. Here, we analyze the emergence of SARS-CoV-2 in Russia in March and April 2020. Combining phylogeographic analysis with travel history data, we estimate that the sampled viral diversity has originated from 67 closely timed introductions into Russia, mostly in late February to early March. All but one of these introductions came from non-Chinese sources, suggesting that border closure with China has helped delay establishment of SARS-CoV-2 in Russia. These introductions resulted in at least 9 distinct Russian lineages corresponding to domestic transmission. A notable transmission cluster corresponded to a nosocomial outbreak at the Vreden hospital in Saint Petersburg; phylodynamic analysis of this cluster reveals multiple (2-4) introductions each giving rise to a large number of cases, with a high initial effective reproduction number of 3.7 (2.5-5.0).

The general goal of this paper is to gather and review several methods from homotopy and combinatorial topology and formal concepts analysis (FCA) and analyze their connections. FCA appears naturally in the problem of combinatorial simplification of simplicial complexes and allows to see a certain duality on a class of simplicial complexes. This duality generalizes Poincare duality on cell subdivisions of manifolds. On the other hand, with the notion of a topological formal context, we review the classical proofs of two basic theorems of homotopy topology: Alexandrov Nerve theorem and Quillen--McCord theorem, which are both important in the applications. A brief overview of the applications of the Nerve theorem in brain studies is given. The focus is made on the task of the external stimuli space reconstruction from the activity of place cells. We propose to use the combination of FCA and topology in the analysis of neural codes. The lattice of formal concepts of a neural code is homotopy equivalent to the nerve complex, but, moreover, it allows to analyse certain implication relations between collections of neural cells.

The most common tools to understand perception of food products are hall-tests, surveys, observations, etc. However to get reliable results these approaches require large samples, making them costly and time-consuming. Furthermore, they are also highly expert-dependent and rely on the assumption that study participants can express their preferences consciously and explicitly. Here we suggested an EEG-based approach to evaluate perceived product similarity in a cross-modal taste-visual task. Two candidate neurometrics measured from Fz electrode were tested: the amplitude of N430-620 from evoked response potentials (ERP) and the power of induced gamma oscillations during 400-600 ms period after visual stimulus presentation. Both suggested metrics showed a strong correlation with the perceived similarity scores at both individual and group levels, however N430-630 had greater inter-subject variability making it less suitable for practical applications. The results based on the power of induced gamma oscillations (N=18) not only reflected the results from traditional hall-tests (N=200) but also allowed better discrimination between different food products.

Admixture is increasingly being recognized as an important factor in evolutionary genetics. The distribution of genomic admixture tracts, and the resulting effects on admixture linkage disequilibrium, can be used to date the timing of admixture between species or populations. However, the theory used for such prediction assumes selective neutrality despite the fact that many famous examples of admixture involve natural selection acting for or against admixture. In this paper, we investigate the effects of positive selection on the distribution of tract lengths. We develop a theoretical framework that relies on approximating the trajectory of the selected allele using a logistic function. By numerically calculating the expected allele trajectory, we also show that the approach can be extended to cases where the logistic approximation is poor due to the effects of genetic drift. Using simulations, we show that the model is highly accurate under most scenarios. We use the model to show that positive selection on average will tend to increase the admixture tract length. However, perhaps counter-intuitively, conditional on the allele frequency at the time of sampling, positive selection will actually produce shorter expected tract lengths. We discuss the consequences of our results in interpreting the timing of the introgression of EPAS1 from Denisovans into the ancestors of Tibetans.

Estimation of the relationship between DNA sequences is one of the most important problems in genomics. Understanding these relationships is central to de- mographic inference, correction of population structure in GWAS, identifying signals of selection etc. The data structure containing the full information about sample genealogy is called the ancestral recombination graph (ARG). However, ARG inference is a very dicult problem, not least due to a very complex state space. In this work we describe a new approach for fast and scalable generation of local tree topologies relating large numbers of haplotypes. Our method is closely related to the estimation of ARG, and captures both local and global properties of an ARG. It is based on a data structure which we call tree consistent PBWT , a modi cation of PBWT data structure intro- duced by R. Durbin (2014). We also explore some methods to estimate the quality of the generated tree topologies and to make inferences based on them. At the end we discuss a probabilistic model which could potentially lead to the estimation of ARG node times.

Whether the motor cortex activation accompanying concrete verbs comprehension is necessary for verbs conceptual processing is still a hotly debated topic in the literature. Answering this question, we examined to what extent the more difficult access to verb semantics requires an additional engagement of cortical motor system in verb generation task. Using power suppression of MEG beta oscillations (15-30 Hz) as an index of sensorimotor activation, we presented to our participants the noun cues which either were strongly associated with a single verb and prompted the fast and effortless verb retrieval, or were weakly associated with multiple verbs and were more difficult to respond to. A whole-brain analysis of beta suppression revealed that the only cortical regions sensitive to the difficulty of semantic access were the higher order motor areas on the medial and lateral surfaces of the frontal lobe. This differential activation of cortical motor system accompanied effortful verb retrieval and preceded the preparation of vocal response for more than 500 milliseconds. Since the mid-frontal frontal brain areas are involved in maintaining abstract representations of actions during their initiating and planning, we argue that our finding supports the view that motor associations contribute to retrieval of verb semantics.

In most countries, women live longer than men. Differences in longevities are country-specific and change over time. We perform a cross-country panel data analysis in developed countries (OECD and EU) to study the gender-longevity gap dependence on various socio-economic indicators and test a number of contradicting theories. We show that a lower gender longevity gap is associated with a higher real GDP per capita, a higher level of urbanization, lower income inequality, lower per capita alcohol consumption and a better ecological environment. An increase in women’s aggregate unemployment rate and a decline in men’s unemployment are associated with a higher gap in life expectancies. The effect of the share of women in parliaments in the gender-longevity gap is estimated to have a U-shape; it has a better descriptive efficiency if taken with a 5-years lag, which approximately corresponds to the length of political cycles.

Human genetic variability is thought to account for a substantial fraction of individual biochemical characteristics — in biomedical sense, of individual drug response. However, only a handful of human genetic variants have been linked to medication outcomes. Here, we combine data on drug-protein interactions and human genome sequences to assess the impact of human variation on their binding affinity. Using data from the complexes of FDA-drugs and drug-like compounds, we predict SNPs substantially affecting the protein-ligand binding affinities. We estimate that an average individual carries ~6 SNPs affecting ~5 different FDA-approved drugs from among all of the approved compounds. SNPs affecting drug-protein binding affinity have low frequency in the population indicating that the genetic component for many ADEs may be highly personalized with each individual carrying a unique set of relevant SNPs. The reduction of ADEs, therefore, may primarily rely on the application of computational genome analysis in the clinic rather than the experimental study of common SNPs.

Despite the success of many countries in increasing energy saving and energy efficiency, the global energy consumption is expected to continue its growth. The main reasons are economic development and population growth happening primarily in developing and emerging economies, especially in India and China. In such circumstances fossil fuels will remain the dominant energy source in the medium and even long run. The present research paper aims at analyzing the current global trends in the energy sector identified through literature review and expert tools, and their influence on Russia. Considering a broad range of factors, the paper determined the following main challenges for the Russian energy sector: tightening competition at international energy markets, the need for comprehensive modernization and stronger energy efficiency measures, the need for technological catch-up in a number of energy sector segments, the need to increase recovery factor at traditional oilfields, and the need to diversify energy mix by increasing the share of renewables. The paper also considers the main rationale for the last challenge that include strengthened security, reliability and sustainability of the Russian energy sector. Among the key preconditions for advancements in renewable energy are improvements in investment climate, modernisation of the central grid and changes in energy policy. The paper is based on the outcomes of the first stage of the Foresight project devoted to renewable energy technologies.

The paper aims to reveal the relationship between improvement in human diet and transition to democracy. The spread of a ‘European diet’ – the diet with historically unprecedented high proportion of animal proteins in daily calories intake – is likely to be one of the factors of regime change since 1992. In contrast to other studies, I regard European diet as an outcome of long historical transformation and show that improvement in nutrition preceded regime change. To get data on nutrients consumption around the world I apply to the Food balance sheets data from FAOSTAT. Based on this data I are able to define a European diet as the one containing animal protein-rich items (mostly, meat and dairy), alcohol beverages and sugar. Using OLS, factor analysis and SEM I test the direct and indirect effects of the European diet on the chance of transition to democracy and find positive impact of improvement in diet on political change. My findings reveal that improvement in diet affects democratization, but not vice versa.

The Foresight study presented in this paper is devoted to the sustainable use of water resources in Russia. The authors analyse possible trajectories of development in the three thematic areas (i) sustainability of water systems; (ii) water use by households and in industry; and (iii) new water products and services. The Foresight methods cover expert interviews and seminars, desk research, and policy analysis. The state and corporate policy recommendations for the water sector offered in this study correspond with the water scenarios earlier identified by Saritas et al.: “Nearly ideal future”, “Losses and accidents”, “Problem conservation”, and “National Priority” [Saritas et al., 2015]. For each of these four scenarios, policy recommendations for water companies were identified covering new solutions (including technological innovations), new values and competencies, organisational changes, modernisation of the infrastructure, financial issues, and legal and regulatory changes. Moreover, we recommend certain policy measures and approaches to state policy in the water sector.  The paper concludes with the main directions and instruments for the sector’s development, which should be planned and implemented jointly by the government and businesses, as well as other stakeholders (organisations and people).

This article considers the uneven positions of school teachers in different regions of the Russian Federation. There exist numerous research works on the relation of school teachers’ salaries to the characteristics of regional educational systems and regional economies. A range of indicators is used to calculate school teachers’ salaries. It is necessary to consider the ratio of the teachers’ salary to the average salary in the region, the latter serving as a target indicator in government programs, in combination with other indicators, such as the ratio of the salary to the price of a fixed set of goods and services and the ratio of the teachers’ salary fund to total regional government expenditures. Research based on cluster data analysis statistical methods allowed the author to distinguish four types of regions. We used official data provided by Russian Federal State Statistics Service and the Russian Federal Treasury. The recommendations developed for each cluster of regions seek to improve the efficiency of the steps aimed at the implementation of the educational policy tasks through differentiating the support measures by the federal government

Midbrain ventral segmental area (VTA) dopaminergic neurons send numerous projections to cortical and sub-cortical areas, and diffusely release dopamine (DA) to their targets. DA neurons display a range of activity modes that vary in frequency and degree of burst ring. Importantly, DA neuronal bursting is associated with a significantly greater degree of DA release than an equivalent tonic activity pattern. Here, we introduce a single compartmental, conductance-based computational model for DA cell activity that captures the behavior of DA neuronal dynamics and examine the multiple factors that underlie DA firing modes: the strength of the SK conductance, the amount of drive, and GABA inhibition. Our results suggest that neurons with low SK conductance are in a fast firing mode, are correlated with burst firing, and require higher levels of applied current before undergoing depolarization block. We go on to consider the role of GABAergic inhibition on an ensemble of dynamical classes of DA neurons and find that strong GABA inhibition suppresses burst firing. Our studies suggest differences in the distribution of the SK conductance and GABA inhibition levels may indicate subclasses of DA neurons within the VTA. We further identify, that by considering alternate potassium dynamics, the dynamics display burst patterns that terminate via depolarization block, akin to those observed in vivo in VTA DA neurons and in substantia nigra pars compacta DA cell preparations under apamin application. In addition, we consider the generation of transient burst ring events that are NMDA-initiated or elicited by a sudden decrease of GABA inhibition, that is, disinhibition.

Humans often adjust their behavior to match the group norms. In this study, we used magnetoencephalographic (MEG) source imaging to investigate the electromagnetic responses to the perceived mismatch between individual and group opinions. After participants were exposed to group opinion that conflicted with their own, we observed an evoked response in the posterior medial prefrontal cortex (pMPFC) occurring around 200 ms, corresponding to the feedback-related negativity (FRN) – a component of the evoked response associated with processing negative feedback and reinforcement learning. This response was accompanied by an increase in  power of theta oscillations (4-8 Hz) over a number of frontal sites (including OFC and pMPFC). The magnitude of both evoked and induced responses to the perceived conflict with social norms was stronger in participants who showed relatively low conformity. Overall, our results suggest that the activation of the pMPFC following conflicts with group opinion, as recoded by MEG, may reflect an enhanced control state – a process complimentary to the reinforcement learning signal in the ventral striatum reported in previous studies of social conformity

Euroregions is an important and quite popular mechanism of cross-border cooperation. Character of institutions development differs essentially between three groups of states, which use this mechanism: old members of the European Union; new members of the European Union (entered the EU after 2003); CIS members. This comparative research is concerned with the main circumstances of euroregions development in three areas noted above. The analyses show the fundamental differences between three Euroregion cases: Oresund, Pskov-Livonia and Dnieper. Those differences are noticeable in legislative basic, financing, cooperation issues, and even in four basic Euroregions principles realizing. Meanwhile we see that after fifteen years of copying the Euroregions in post-soviet countries the positive shifts occur in CIS members’ government perception and in the decision making process.