The long-term relationship between temperature and hydroclimate has remained uncertain due to the short length of instrumental measurements and inconsistent results from climate model simulations. This lack of understanding is particularly critical with regard to projected drought and flood risks. Here we assess warm-season co-variability patterns between temperature and hydroclimate over Europe back to 850 CE using instrumental measurements, tree-ring based reconstructions, and climate model simulations. We find that the temperature–hydroclimate relationship in both the instrumental and reconstructed data turns more positive at lower frequencies, but less so in model simulations, with a dipole emerging between positive (warm and wet) and negative (warm and dry) associations in northern and southern Europe, respectively. Compared to instrumental data, models reveal a more negative co-variability across all timescales, while reconstructions exhibit a more positive co-variability. Despite the observed differences in the temperature–hydroclimate co-variability patterns in instrumental, reconstructed and model simulated data, we find that all data types share relatively similar phase-relationships between temperature and hydroclimate, indicating the common influence of external forcing. The co-variability between temperature and soil moisture in the model simulations is overestimated, implying a possible overestimation of temperature-driven future drought risks.
Reference genes selection is one of the most important stages in qPCR data normalization when a problem of quantitative determination of gene expression is addressed. Stability of gene expression level in all experimental conditions is a basic criterion for the reference gene selection. Over the past decade a lot of publications concerning validation methods of suitable reference genes appeared. In this paper, the main approaches (∆Ct, geNorm, qBase and Haller’s equivalence test) were applied for the reference genes identi? fication in HeLa cell line which is one of the most popular cellular models. Expression stability of seven can? didate genes (HPRT1, ACTB, GAPDH, RPS18, HSPC3, UBC and SDHA) was determined at standard condi? tions, under heat shock and during relaxation. The genes RPS18 and HSPC3 were chosen as reference after the combination of all the validation methods
It has been presented that Western cultures (USA, Western Europe) are mostly characterized by competitive forms of social interaction, whereas Eastern cultures (Japan, China, Russia) are mostly characterized by cooperative forms. It has also been stated that thinking in Eastern countries is predominantly holistic and in Western countries analytic. Based on this, we hypothesized that subjects with analytic vs. holistic thinking styles show differences in decision making in different types of social interaction conditions. We investigated behavioural and brain-activity differences between subjects with analytic and holistic thinking during a choice reaction time (ChRT) task, wherein the subjects either cooperated, competed (in pairs), or performed the task without interaction with other participants. Healthy Russian subjects (N=78) were divided into two groups based on having analytic or holistic thinking as determined with an established questionnaire. We measured reaction times as well as event-related brain potentials. There were significant differences between the interaction conditions in task performance between subjects with analytic and holistic thinking. Both behavioral performance and physiological measures exhibited higher variance in holistic than in analytic subjects. Differences in amplitude and P300 latency suggest that decision making was easier for the holistic subjects in the cooperation condition, in contrast to analytic subjects for whom decision making based on these measures seemed to be easier in the competition condition. The P300 amplitude was higher in the individual condition as compared with the collective conditions. Overall, our results support the notion that the brains of analytic and holistic subjects work differently in different types of social interaction conditions.
Near-annual pollen records for the last 100 years were obtained from a 65-cm peat monolith from a raised peat bog in the Central Forest State Natural Biosphere Reserve (southern part of the Valdai Hills, European Russia) and compared with the available long-term meteorological observations. An age–depth model for the peat monolith was constructed by 210Pb and 137Cs dating. Cross-correlation and the Granger causality analysis indicated a broad range of statistically significant correlations between the pollen accumulation rate (PAR) of the main forest-forming trees and shrubs (Picea, Pinus, Betula, Tilia, Quercus, Ulmus, Alnus, and Corylus) and the air temperature and precipitation during the previous 3 years. Results showed that high air temperatures during the growing season (May–September) in the year prior to the flowering led to an increase in pollen productivity of the main tree species. The statistically significant correlation between the PAR of trees and shrubs and winter precipitation of the current and previous years could reflect the influence of winter precipitation on soil water availability and as a result on tree growth and functioning in the spring.
Evolutionary games are used in various elds stretching from economics to biology. Most assume a constant payoff matrix, although some works also consider dynamic payoff matrices. In this article we propose a possibility of switching the system between two regimes with different sets of payoff matrices. Such a model can qualitatively describe the development of bacterial or cancer cells with a mutator gene present. A nite population evolutionary game is studied. The model describes the simplest version of annealed disorder in the payoff matrix and is exactly solvable. We analyze the dynamics of the model, and derive the equations for both the maximum and the variance of the distribution by applying the Hamilton-Jacobi formalism. Therefore, we present an exactly solvable version of an evolutionary game with annealed noise in the payoff matrix.
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.
Statistical estimates of internal waves in different regions of theWorld Ocean are discussed. It is found that the observed exceedance probability of large-amplitude internal waves in most cases can be described by the Poisson law, which is one of the typical laws of extreme statistics. Detailed analysis of the statistical properties of internal waves in several regions of theWorld Ocean has been performed: tropical part of the Atlantic Ocean, northwestern shelf of Australia, the Mediterranean Sea near the Egyptian coast, and the Yellow Sea.
Linguistic processing is based on a close collaboration between temporal and frontal regions connected by two pathways: the “dorsal” and “ventral pathways” (assumed to support phonological and semantic processing, respectively, in adults). We investigated here the development of these pathways at the onset of language acquisition, during the first post-natal weeks, using cross-sectional diffusion imaging in 21 healthy infants (6–22 weeks of age) and 17 young adults. We compared the bundle organization and microstructure at these two ages using tractography and original clustering analyses of diffusion tensor imaging parameters. We observed structural similarities between both groups, especially concerning the dorsal/ventral pathway segregation and the arcuate fasciculus asymmetry. We further highlighted the developmental tempos of the linguistic bundles: The ventral pathway maturation was more advanced than the dorsal pathway maturation, but the latter catches up during the first post-natal months. Its fast development during this period might relate to the learning of speech cross-modal representations and to the first combinatorial analyses of the speech input.
The aim of this study was to develop a paradigm for obtaining a multi-feature profile for central auditory processing of different magnitudes of prosodic and phonetic changes in speech sounds. We recorded the MMNs to three vowel identity changes, three magnitudes of changes in intensity, and vowel duration as well as to two magnitudes of pitch changes from semi-synthetic vowels in 34min. Furthermore, we examined how the type and magnitude of deviation affect the size and timing of the MMN. All sound changes elicited statistically significant MMN responses, with the MMNamplitudes increasing with an increase in sound deviance. Importantly, the MMN amplitudes for the vowel changes reflected the differences between the phonemes, as did the MMNs to vowel-duration changes reflect the categorization of these sounds to short and long vowel categories, which are meaningful in the Finnish language. This new multi-feature MMN paradigm is suitable for investigating the central auditory processing of different magnitudes of speech-sound changes and can be used, for instance, in the investigation of pre-attentive phoneme categorization. The paradigm is especially useful for studying speech and language disorders in general, language development, and evolution of phoneme categories early in life, as well as brain plasticity during native or second language learning
How do human brain networks react to dynamic changes in the sensory environment? We measured rapid changes in brain network organization in response to brief, discrete, salient auditory stimuli. We estimated network topology and distance parameters in the immediate central response period, <1 s following auditory presentation of standard tones interspersed with occasional deviant tones in a mismatch-negativity (MMN) paradigm, using magnetoencephalography (MEG) to measure synchronization of high-frequency (gamma band; 33-64 Hz) oscillations in healthy volunteers. We found that global small-world parameters of the networks were conserved between the standard and deviant stimuli. However, surprising or unexpected auditory changes were associated with local changes in clustering of connections between temporal and frontal cortical areas and with increased interlobar, long-distance synchronization during the 120- to 250-ms epoch (coinciding with the MMN-evoked response). Network analysis of human MEG data can resolve fast local topological reconfiguration and more long-range synchronization of high-frequency networks as a systems-level representation of the brain's immediate response to salient stimuli in the dynamically changing sensory environment.
Phase synchronization among neuronal oscillations within the same frequency band has been hypothesized to be a major mechanism for communication between different brain areas. On the other hand, cross-frequency communications are more flexible allowing interactions between oscillations with different frequencies. Among such cross-frequency interactions amplitude-to-amplitude interactions are of a special interest as they show how the strength of spatial synchronization in different neuronal populations relates to each other during a given task. While, previously, amplitude-to-amplitude correlations were studied primarily on the sensor level, we present a source separation approach using spatial filters which maximize the correlation between the envelopes of brain oscillations recorded with electro-/magnetoencephalography (EEG/MEG) or intracranial multichannel recordings. Our approach, which is called canonical source power correlation analysis (cSPoC), is thereby capable of extracting genuine brain oscillations solely based on their assumed coupling behavior even when the signal-to-noise ratio of the signals is low. In addition to using cSPoC for the analysis of cross-frequency interactions in the same subject, we show that it can also be utilized for studying amplitude dynamics of neuronal oscillations across subjects. We assess the performance of cSPoC in simulations as well as in three distinctively different analysis scenarios of real EEG data, each involving several subjects. In the simulations, cSPoC outperforms unsupervised state-of-the-art approaches. In the analysis of real EEG recordings, we demonstrate excellent unsupervised discovery of meaningful power-to-power couplings, within as well as across subjects and frequency bands.
National science and technology priority-setting has been an important and regular exercise performed by developed and many developing countries. This is very relevant for the conservative energy industry with long investment cycles. The future of energy is shaped by today's investments in research and development.
The Strategy for Science and Technology Development of the Russian Federation (2016) features seven priorities, one of which is related to “the transition to environmentally friendly and resource-saving energy industry”. The paper describes the foresight study of this energy priority that was launched to identify the focus of related future comprehensive science and technology funding programs. The design, methods and outcomes of this study that frame the future science and technology development in Russia's energy industry are discussed together with research and policy implications.
Chromosomes are key players of cell physiology, their dynamics provides valuable information about its physical organization. In both prokaryotes and eukaryotes, the short-time motion of chromosomal loci has been described with a Rouse model in a simple or viscoelastic medium. However, little emphasis has been put on the influence of the folded organization of chromosomes on the local dynamics. Clearly, stress propagation, and thus dynamics, must be affected by such organization, but a theory allowing us to extract such information from data, e.g., on two-point correlations, is lacking. Here, we describe a theoretical framework able to answer this general polymer dynamics question. We provide a scaling analysis of the stress-propagation time between two loci at a given arclength distance along the chromosomal coordinate. The results suggest a precise way to assess folding information from the dynamical coupling of chromosome segments. Additionally, we realize this framework in a specific model of a polymer whose long-range interactions are designed to make it fold in a fractal way and immersed in a medium characterized by subdiffusive fractional Langevin motion with a tunable scaling exponent. This allows us to derive explicit analytical expressions for the correlation functions.
In Parkinson's disease (PD) levodopa-associated changes in the power and long-range temporal correlations of beta oscillations have been demonstrated, yet the presence and modulation of genuine connectivity in local field potentials (LFP) recorded from the subthalamic nucleus (STN) remains an open question. The present study investigated LFP recorded bilaterally from the STN at wakeful rest in ten patients with PD after overnight withdrawal of levodopa (OFF) and after a single dose levodopa administration (ON). We utilized connectivity measures being insensitive to volume conduction (functional connectivity: non-zero imaginary part of coherency; effective connectivity: phase-slope index). We demonstrated the presence of neuronal interactions in the frequency range of 10-30 Hz in STN-LFP without a preferential directionality of interactions between different contacts along the electrode tracks. While the direction of neuronal interactions per se was preserved after levodopa administration, functional connectivity and the ventral-dorsal information flow were modulated by medication. The OFF-ON differences in functional connectivity were correlated with the levodopa-induced improvement in clinical Unified Parkinson's Disease Rating Scale scores. We hypothesize that regional neuronal interactions, as reflected in STN-LFP connectivity, might represent a basis for the intra-nuclear spatial specificity of deep brain stimulation. Moreover, our results suggest the potential use of volume conduction-insensitive measures of connectivity in STN-LFP as a marker of clinical motor symptoms in PD.
Background Up-to-date evidence on levels and trends for age-sex-specific all-cause and cause-specific mortality is essential for the formation of global, regional, and national health policies. In the Global Burden of Disease Study 2013 (GBD 2013) we estimated yearly deaths for 188 countries between 1990, and 2013. We used the results to assess whether there is epidemiological convergence across countries. Methods We estimated age-sex-specific all-cause mortality using the GBD 2010 methods with some refinements to improve accuracy applied to an updated database of vital registration, survey, and census data. We generally estimated cause of death as in the GBD 2010. Key improvements included the addition of more recent vital registration data for 72 countries, an updated verbal autopsy literature review, two new and detailed data systems for China, and more detail for Mexico, UK, Turkey, and Russia. We improved statistical models for garbage code redistribution. We used six different modelling strategies across the 240 causes; cause of death ensemble modelling (CODEm) was the dominant strategy for causes with sufficient information. Trends for Alzheimer's disease and other dementias were informed by meta-regression of prevalence studies. For pathogen-specific causes of diarrhoea and lower respiratory infections we used a counterfactual approach. We computed two measures of convergence (inequality) across countries: the average relative difference across all pairs of countries (Gini coefficient) and the average absolute difference across countries. To summarise broad findings, we used multiple decrement life-tables to decompose probabilities of death from birth to exact age 15 years, from exact age 15 years to exact age 50 years, and from exact age 50 years to exact age 75 years, and life expectancy at birth into major causes. For all quantities reported, we computed 95% uncertainty intervals (UIs). We constrained cause-specific fractions within each age-sex-country-year group to sum to all-cause mortality based on draws from the uncertainty distributions. Findings Global life expectancy for both sexes increased from 65·3 years (UI 65·0–65·6) in 1990, to 71·5 years (UI 71·0–71·9) in 2013, while the number of deaths increased from 47·5 million (UI 46·8–48·2) to 54·9 million (UI 53·6–56·3) over the same interval. Global progress masked variation by age and sex: for children, average absolute differences between countries decreased but relative differences increased. For women aged 25–39 years and older than 75 years and for men aged 20–49 years and 65 years and older, both absolute and relative differences increased. Decomposition of global and regional life expectancy showed the prominent role of reductions in age-standardised death rates for cardiovascular diseases and cancers in high-income regions, and reductions in child deaths from diarrhoea, lower respiratory infections, and neonatal causes in low-income regions. HIV/AIDS reduced life expectancy in southern sub-Saharan Africa. For most communicable causes of death both numbers of deaths and age-standardised death rates fell whereas for most non-communicable causes, demographic shifts have increased numbers of deaths but decreased age-standardised death rates. Global deaths from injury increased by 10·7%, from 4·3 million deaths in 1990 to 4·8 million in 2013; but age-standardised rates declined over the same period by 21%. For some causes of more than 100 000 deaths per year in 2013, age-standardised death rates increased between 1990 and 2013, including HIV/AIDS, pancreatic cancer, atrial fibrillation and flutter, drug use disorders, diabetes, chronic kidney disease, and sickle-cell anaemias. Diarrhoeal diseases, lower respiratory infections, neonatal causes, and malaria are still in the top five causes of death in children younger than 5 years. The most important pathogens are rotavirus for diarrhoea and pneumococcus for lower respiratory infections. Country-specific probabilities of death over three phases of life were substantially varied between and within regions. Interpretation For most countries, the general pattern of reductions in age-sex specific mortality has been associated with a progressive shift towards a larger share of the remaining deaths caused by non-communicable disease and injuries. Assessing epidemiological convergence across countries depends on whether an absolute or relative measure of inequality is used. Nevertheless, age-standardised death rates for seven substantial causes are increasing, suggesting the potential for reversals in some countries. Important gaps exist in the empirical data for cause of death estimates for some countries; for example, no national data for India are available for the past decade.
Three Lagrangian invariants are shown to exist for flows in the equatorial region in the β - plane approximation.
They extend the Cauchy invariants to a non-rotating fluid. The relationship between these generalized invariants
and the results following from Kelvin's and Ertel's theorems is ascertained. Explicit expressions of the invariants
for equatorially trapped waves and equatorial Gerstner waves are presented.
In this Letter, the generalized Wiedemann-Franz law for the non-isothermic quasi-neutral plasma with developed ion-acoustic turbulence is proved. This law determines the relationship between electrical and thermal conductivities in a plasma with well-developed ion-acoustic turbulence. The anomalously low thermal conductivity, which leads to the formation of high temperature gradients in the zone of the temperature jump, is explained. Results are used to explain some properties of the solar chromosphere-corona transition region.
Differential RNA-sequencing (dRNA-seq) is indispensable for determination of primary transcriptomes. However, using dRNA-seq data to map transcriptional start sites (TSSs) and promoters genome-wide is a bioinformatics challenge. We performed dRNA-seq of Bradyrhizobium japonicum USDA 110, the nitrogen-fixing symbiont of soybean, and developed algorithms to map TSSs and promoters.
A specialized machine learning procedure for TSS recognition allowed us to map 15,923 TSSs: 14,360 in free-living bacteria, 4329 in symbiosis with soybean and 2766 in both conditions. Further, we provide proteomic evidence for 4090 proteins, among them 107 proteins corresponding to new genes and 178 proteins with N-termini different from the existing annotation (72 and 109 of them with TSS support, respectively). Guided by proteomics evidence, previously identified TSSs and TSSs experimentally validated here, we assign a score threshold to flag 14 % of the mapped TSSs as a class of lower confidence. However, this class of lower confidence contains valid TSSs of low-abundant transcripts. Moreover, we developed a de novo algorithm to identify promoter motifs upstream of mapped TSSs, which is publicly available, and found motifs mainly used in symbiosis (similar to RpoN-dependent promoters) or under both conditions (similar to RpoD-dependent promoters). Mapped TSSs and putative promoters, proteomic evidence and updated gene annotation were combined into an annotation file.
The genome-wide TSS and promoter maps along with the extended genome annotation of B. japonicum represent a valuable resource for future systems biology studies and for detailed analyses of individual non-coding transcripts and ORFs. Our data will also provide new insights into bacterial gene regulation during the agriculturally important symbiosis between rhizobia and legumes.
The genome of Caldithrix abyssi, the first cultivated representative of a phylum-level bacterial lineage, was sequenced within the framework of Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. The genomic analysis revealed mechanisms allowing this anaerobic bacterium to ferment peptides or to implement nitrate reduction with acetate or molecular hydrogen as electron donors. The genome encoded five different [NiFe]- and [FeFe]-hydrogenases, one of which, group 1 [NiFe]-hydrogenase, is presumably involved in lithoheterotrophic growth, three other produce H2 during fermentation, and one is apparently bidirectional. The ability to reduce nitrate is determined by a nitrate reductase of the Nap family, while nitrite reduction to ammonia is presumably catalyzed by an octaheme cytochrome c nitrite reductase εHao. The genome contained genes of respiratory polysulfide/thiosulfate reductase, however, elemental sulfur and thiosulfate were not used as the electron acceptors for anaerobic respiration with acetate or H2, probably due to the lack of the gene of the maturation protein. Nevertheless, elemental sulfur and thiosulfate stimulated growth on fermentable substrates (peptides), being reduced to sulfide, most probably through the action of the cytoplasmic sulfide dehydrogenase and/or NAD(P)-dependent [NiFe]-hydrogenase (sulfhydrogenase) encoded by the genome. Surprisingly, the genome of this anaerobic microorganism encoded all genes for cytochrome c oxidase, however, its maturation machinery seems to be non-operational due to genomic rearrangements of supplementary genes. Despite the fact that sugars were not among the substrates reported when C. abyssi was first described, our genomic analysis revealed multiple genes of glycoside hydrolases, and some of them were predicted to be secreted. This finding aided in bringing out four carbohydrates that supported the growth of C. abyssi: starch, cellobiose, glucomannan and xyloglucan. The genomic analysis demonstrated the ability of C. abyssi to synthesize nucleotides and most amino acids and vitamins. Finally, the genomic sequence allowed us to perform a phylogenomic analysis, based on 38 protein sequences, which confirmed the deep branching of this lineage and justified the proposal of a novel phylum Calditrichaeota.
The Kets, an ethnic group in the Yenisei River basin, Russia, are considered the last nomadic hunter-gatherers of Siberia, and Ket language has no transparent affiliation with any language family. We investigated connections between the Kets and Siberian and North American populations, with emphasis on the Mal'ta and Paleo-Eskimo ancient genomes, using original data from 46 unrelated samples of Kets and 42 samples of their neighboring ethnic groups (Uralic-speaking Nganasans, Enets, and Selkups). We genotyped over 130,000 autosomal SNPs, identified mitochondrial and Y-chromosomal haplogroups, and performed high-coverage genome sequencing of two Ket individuals. We established that Nganasans, Kets, Selkups, and Yukaghirs form a cluster of populations most closely related to Paleo-Eskimos in Siberia (not considering indigenous populations of Chukotka and Kamchatka). Kets are closely related to modern Selkups and to some Bronze and Iron Age populations of the Altai region, with all these groups sharing a high degree of Mal'ta ancestry. Implications of these findings for the linguistic hypothesis uniting Ket and Na-Dene languages into a language macrofamily are discussed.