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Regular version of the site
Of all publications in the section: 646
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Article
Kuznetsova K., Trufanov P., Moysa A. et al. Rapid Communications in Mass Spectrometry. 2016. Vol. 30. No. 11. P. 1323-1331.

One of the problems in proteogenomic research aimed at identification of variant peptides is the presence of peptides with amino acid isomers of different origin in the analyzed samples. Among the most challenging examples are peptides with threonine and isothreonine (homoserine) in their sequences. Indeed, the latter residue may appear in vitro as a methionine substitution during sample preparation for shotgun proteome analysis. Yet, this substitution of Met to isoThr is not encoded genetically and should be unambiguously distinguished from, e.g., point mutations in proteins that result in Met conversion to Thr.

METHODS:

In this work we compared tandem mass (MS/MS) spectra produced by an Orbitrap mass spectrometer of Thr- and isoThr-containing tryptic peptides and found a distinctive feature in their collisionally activated fragmentation patterns.

RESULTS:

Up to 84% of MS/MS spectra for peptides containing isoThr residues have been positively specified. We also studied the differences in retention times for peptides containing Thr isoforms that can be further used for their distinction.

CONCLUSIONS:

Threonine can be distinguished from isothreonine by its retention time and HCD fragmentation pattern, specifically relative intensity of the bn - product ion, which can be further used in proteomic research

Added: Mar 14, 2018
Article
Alyushin A. Axiomathes. 2010. Vol. 20. No. 4. P. 439-460.

My goal is to conceive how the reality would look like for hypothetical creatures that supposedly perceive on time scales much faster or much slower that of us humans. To attain the goal, I propose modelling in two steps. At step we have to single out a uni“ed parameter that sets time scale of perception. Changing substantially the value of the parameter would mean changing scale. argue that the required parameter is duration of discrete perceptive frames, snapshots, whose sequencing constitutes perceptive process. I show that different standard durations of perceptive frames is the ground for differences in perceptive time scales of various animals. Abnormally changed duration of perceptive frames is the cause of the effect of distorted subjective time observed by humans under some conditions. Now comes step two of the modelling. By inserting some arbitrary duration of a perceptive frame, we set a hypothetical scale and thus emulate viewpoint for virtual observation of the reality in a wider or narrower angle embracing events in time. Like changing lenses of a microscope, viewing reality different temporal scales makes certain features of reality manifested, others veiled. These are, in particular, features of life. If we observe an object in an inappropriate interval, we may not notice the very essence of a process it is undergoing.

Added: Jan 20, 2013
Article
Nechaev S., Tamm M., Valba O. V. et al. Journal of Statistical Mechanics: Theory and Experiment. 2014. No. 12. P. 12004.

In this paper, we investigate analytical properties of planar matching on a line in the disordered Bernoulli model. This model is characterized by a topological phase transition, yielding the complete planar matching solutions only above a critical density threshold. We develop a combinatorial procedure of arcs expansion that explicitly takes into account the contribution of short arcs, and allows to obtain an accurate analytical estimation of the critical value by reducing the global constrained problem to a set of local ones. As an application to the physics of the RNA secondary structures, we suggest generalized models that incorporate a one-to-one correspondence between the contact matrix and the nucleotide sequence, thus giving sense to the notion of effective non-integer alphabets

Added: Oct 23, 2014
Article
Kabachnick P., Grabowska M., Regulska J. et al. Gender, Place and Culture: A Journal of Feminist Geography. 2013. Vol. 20. No. 6. P. 773-793.

Over 200,000 people became internally displaced after several violent conflicts in the early 1990s in Georgia. For many internally displaced persons (IDPs), gender relations have been transformed significantly. This translates to many women taking on the role of breadwinner for their family, which often is accompanied by the process of demasculinization for men. In this article, we examine the construction of masculinities and analyze the gendered processes of displacement and living in post-displacement for Georgian IDPs from Abkhazia. We identify the formation of ‘traumatic masculinities’ as a result of the threats to, though not usurpation of, hegemonic masculinities. Drawing on interviews, we highlight how IDPs conceptualize gender norms and masculinities in Georgia. Despite the disruptions that displacement has brought about, with the subsequent challenges to IDPs’ ideal masculine roles, the discourses of hegemonic masculinities still predominate amongst IDPs. We further illustrate this point by identifying two separate gendered discourses of legitimization that attempt to reconcile hegemonic masculinities with the current contexts and circumstances that IDPs face. These new traumatic masculinities do coexist with hegemonic masculinities, although the latter are reformed and redefined as a result of the new contexts and new places within which they are performed.

Added: Mar 21, 2013
Article
Зайцев А., Бабейко А., Куркин А. А. и др. Izvestiya, Atmospheric and Oceanic Physics. 2019. Т. 55. № 5. С. 462-469.

Tsunami forecast possibilities for areas with a small base of historical tsunamis have been discussed using the Probabilistic Tsunami Hazard Assessment (PTHA) method, which is based on a statistical analysis of a sufficiently large number of real and predictive earthquakes with a subsequent calculation of possible tsunami waves. This method has been used for a long-term tsunami hazard assessment on the Mediterranean coast of Egypt. The predicted wave heights have been shown to vary along the coastline due to the inhomogeneity of the coastal topography and specific features of the tsunami radiation pattern in the sea. The predicted wave heights for 1000 years vary in the range between 0.8 and 3.4 m.

Added: Oct 30, 2019
Article
Pelinovsky E., Didenkulova I. Pure and Applied Geophysics. 2018. Vol. 175. No. 4. P. 1387-1391.

We solve analytically a nonlinear problem of shallow water theory for the tsunami wave run-up on a vertical wall in tidal environment. Shown that the tide can be considered static in the process of tsunami wave run-up. In this approximation, it is possible to obtain the exact solution for the run-up height as a function of the incident wave height. This allows us to investigate the tide influence on the run-up characteristics.

Added: Oct 21, 2018
Article
Ylinen S., Nora A., Leminen A. et al. Cerebral Cortex. 2014. Vol. doi: 10.1093/cercor/bht351. P. 1-11.

Speech production, both overt and covert, down-regulates the activation of auditory cortex. This is thought to be due to forward prediction of the sensory consequences of speech, contributing to a feedback control mechanism for speech production. Critically, however, these regulatory effects should be specific to speech content to enable accurate speech monitoring. To determine the extent to which such forward prediction is content-specific, we recorded the brain's neuromagnetic responses to heard multisyllabic pseudowords during covert rehearsal in working memory, contrasted with a control task. The cortical auditory processing of target syllables was significantly suppressed during rehearsal compared with control, but only when they matched the rehearsed items. This critical specificity to speech content enables accurate speech monitoring by forward prediction, as proposed by current models of speech production. The one-to-one phonological motor-to-auditory mappings also appear to serve the maintenance of information in phonological working memory. Further findings of right-hemispheric suppression in the case of whole-item matches and left-hemispheric enhancement for last-syllable mismatches suggest that speech production is monitored by 2 auditory-motor circuits operating on different timescales: Finer grain in the left versus coarser grain in the right hemisphere. Taken together, our findings provide hemisphere-specific evidence of the interface between inner and heard speech.

Added: Oct 23, 2014
Article
MacGregor L. J., Difrancesco S., Pulvermuller F. et al. Brain Topography. 2015. Vol. 28. No. 2. P. 279-291.

Effects of intensive language action therapy (ILAT) on automatic language processing were assessed using Magnetoencephalography (MEG). Auditory magnetic mismatch negativity (MMNm) responses to words and pseudowords were recorded in twelve patients with chronic aphasia before and immediately after two weeks of ILAT. Following therapy, Patients showed significant clinical improvements of auditory comprehension as measured by the Token Test and in word retrieval and naming as measured by the Boston Naming Test. Neuromagnetic responses dissociated between meaningful words and meaningless word-like stimuli ultra-rapidly, approximately 50 ms after acoustic information first allowed for stimulus identification. Over treatment, there was a significant increase in the left-lateralisation of this early word-elicited activation, observed in perilesional fronto-temporal regions. No comparable change was seen for pseudowords. The results may reflect successful, therapy-induced, language restitution in the left hemisphere.

Added: Oct 23, 2014
Article
MacGregor L. J., Pulvermuller F., van Casteren M. et al. Nature Communications. 2012. Vol. 3. No. 711. P. DOI: 10.1038/ncomms1715.

Rapid information processing in the human brain is vital to survival in a highly dynamic environment. The key tool humans use to exchange information is spoken language, but the exact speed of the neuronal mechanisms underpinning speech comprehension is still unknown. Here we investigate the time course of neuro-lexical processing by analyzing neuromagnetic brain activity elicited in response to psycholinguistically and acoustically matched groups of words and pseudowords. We show an ultra-early dissociation in cortical activation elicited by these stimulus types, emerging ∼50 ms after acoustic information required for word identification first becomes available. This dissociation is the earliest brain signature of lexical processing of words so far reported, and may help explain the evolutionary advantage of human spoken language.

Added: Oct 23, 2014
Article
Kust G., Andreeva O., Lobkovskiy V. et al. Environmental Science and Policy. 2018. Vol. 89. P. 348-356.
Added: Apr 20, 2020
Article
Loganathan N., Bowers G. M., Ngouana-Wakou B. F. et al. Physical Chemistry Chemical Physics. 2019. Vol. 21. P. 6917-6924 .

The interactions among fluid species such as H2O, CO2, and CH4 confined in nano- and meso-pores in shales and other rocks is of central concern to understanding the chemical behavior and transport properties of these species in the earth’s subsurface and is of special concern to geological C-sequestration and enhanced production of oil and natural gas. The behavior of CO2, and CH4 are less well understood than that of H2O. This paper presents the results of a computational modeling study of the partitioning of CO2 and CH4 between bulk fluid and nano- and meso-pores bounded by the common clay mineral montmorillonite. The calculations were done at 323 K and a total fluid pressure of 124 bars using a novel approach (constant reservoir composition molecular dynamics, CRC-MD) that uses bias forces to maintain a constant composition in the fluid external to the pore. This purely MD approach overcomes the difficulties in making stochastic particle insertion-deletion moves in dense fluids encountered in grand canonical Monte Carlo and related hybrid approaches. The results show that both the basal siloxane surfaces and protonated broken edge surfaces of montmorillonite both prefer CO2 relative to CH4 suggesting that methods of enhanced oil and gas production using CO2 will readily displace CH4 from such pores. This preference for CO2 is due to its preferred interaction with the surfaces and extends to approximately 20 Å from them.

Added: Nov 2, 2019
Article
Maex R., Grinevich V., Grinevich V. et al. ACS Chem Neurosci. 2014. Vol. 15. No. 5. P. 1032-1040.

Neuronal nicotinic acetylcholine receptors (NNRs) of the α7 subtype have been shown to contribute to the release of dopamine in the nucleus accumbens. The site of action and the underlying mechanism, however, are unclear. Here we applied a circuit modeling approach, supported by electrochemical in vivo recordings, to clarify this issue. Modeling revealed two potential mechanisms for the drop in accumbal dopamine efflux evoked by the selective α7 partial agonist TC-7020. TC-7020 could desensitize α7 NNRs located predominantly on dopamine neurons or glutamatergic afferents to them or, alternatively, activate α7 NNRs located on the glutamatergic afferents to GABAergic interneurons in the ventral tegmental area. Only the model based on desensitization, however, was able to explain the neutralizing effect of coapplied PNU-120596, a positive allosteric modulator. According to our results, the most likely sites of action are the preterminal α7 NNRs controlling glutamate release from cortical afferents to the nucleus accumbens. These findings offer a rationale for the further investigation of α7 NNR agonists as therapy for diseases associated with enhanced mesolimbic dopaminergic tone, such as schizophrenia and addiction

Added: Feb 17, 2015
Article
Kolokolov I., Lebedev V., Gamba A. et al. Journal of Statistical Mechanics: Theory and Experiment. 2009. P. P02019.
Cell polarization plays a central role in the development of complex organisms. It has been recently shown that cell polarization may follow from the proximity to a phase separation instability in a bistable network of chemical reactions. An example which has been thoroughly studied is the formation of signaling domains during eukaryotic chemotaxis. In this case, the process of domain growth may be described by the use of a constrained time-dependent Landau–Ginzburg equation, admitting scale-invariant solutions `a la Lifshitz and Slyozov. The constraint results here from a mechanism of fast cycling of molecules between a cytosolic, inactive state and a membrane-bound, active state, which dynamically tunes the chemical potential for membrane binding to a value corresponding to the coexistence of different phases on the cell membrane. We provide here a universal description of this process both in the presence and in the absence of a gradient in the external activation field. Universal power laws are derived for the time needed for the cell to polarize in a chemotactic gradient, and for the value of the smallest detectable gradient. We also describe a concrete realization of our scheme based on the analysis of available biochemical and biophysical data.
Added: Feb 7, 2017
Article
Baulin E., Victor Yacovlev, Khachko D. et al. Database: the journal of biological databases and curation. 2016.

The Universe of RNA Structures DataBase (URSDB) stores information obtained from all RNA-containing PDB entries (2935 entries in October 2015). The content of the database is updated regularly. The database consists of 51 tables containing indexed data on various elements of the RNA structures. The database provides a web interface allowing user to select a subset of structures with desired features and to obtain various statistical data for a selected subset of structures or for all structures. In particular, one can easily obtain statistics on geometric parameters of base pairs, on structural motifs (stems, loops, etc.) or on different types of pseudoknots. The user can also view and get information on an individual structure or its selected parts, e.g. RNA–protein hydrogen bonds. URSDB employs a new original definition of loops in RNA structures. That definition fits both pseudoknot-free and pseudoknotted secondary structures and coincides with the classical definition in case of pseudoknot-free structures. To our knowledge, URSDB is the first database supporting searches based on topological classification of pseudoknots and on extended loop classification.

Added: Oct 28, 2016
Article
Adushkin V. V., Nifadiev V. I., Chen B. B. et al. Doklady Earth Sciences. 2019. Vol. 487. No. 1. P. 841-845.

Based on the data of experimental studies of wave disturbances in the Earth's atmosphere before and after the earthquakes in Uzbekistan (May 26, 2013) and Kyrgyzstan (January 8, 2007), earlier unknown changes in the parameters of internal gravity waves are revealed. These changes were manifested during the period of five days before the earthquake and in certain cases can be used for short-term prediction of the time when seismic events are to occur.

Added: Sep 12, 2019
Article
Kutuzov S. Frontiers in Earth Science. 2019. Vol. 7. P. 1-16.

This study describes the analysis of changes in area and volume of the Mt.Elbrus glacier system, Central Caucasus from 1997 to 2017. It is based on helicopter-borne ice thickness measurements, comparison of high-resolution imagery and two digital elevation models (DEMs) with 10 m resolution. More than 250 km of ground-penetrating radar (GPR) profiles of ice thickness with reliable reflections were obtained. The total volume of Mt. Elbrus glaciers was 5.03 ± 0.85 km3 of ice in 2017. Our results show that 68% of the total ice volume is concentrated below 4,000 m a.s.l. where the average ice thickness was 44.6 ± 7.3 m, 18% of the volume lies within 4,000–4,500 m a.s.l. (thickness of 41.2 ± 7.3 m), and just 14% lies above 4,500 m a.s.l. (thickness of 29.7 ± 6.7 m). The glacier-covered area of Mt. Elbrus decreased from 125.76 ± 0.65 km2 in 1997 to 112.20 ± 0.58 km2 in 2017, a reduction of 10.8%. Over the same period the volume decreased by 22.8%. The mass balance of the Elbrus glaciers decreased by −0.55 ± 0.04 m w.e. a−1 from 1997 to 2017. Mass balance on west-oriented glaciers is less negative than on east-and south-oriented glaciers where mass balance is most negative. The mass balance of the east-oriented Djikiugankez glacier decreased at the fastest average rate (−0.97 ± 0.07 m w.e. a−1). This glacier contains 28% of the total Elbrus glacier system ice volume, most of which is concentrated below 4,000 m a.s.l. Only one small glacier on the western slope demonstrated mass gain. Our results match well with the long term direct mass balance measurements on the Garabashi glacier on Elbrus which lost 12.58 m w.e. and 12.92 ± 0.95 m w.e. between 1997 and 2017 estimated by glaciological and geodetic method, respectively. The rate of Elbrus glacier mass loss tripled in 1997-2017 compared with the 1957-1997 period.

Added: Sep 4, 2019
Article
Butovskaya M. Scientific Reports. 2017. Vol. 7. No. 1622. P. 1-9.

It has been suggested that the preference for low WHRs evolved because low WHR provided a cue to female reproductive status and health, and therefore to her reproductive value. The present study aimed to test whether WHR might indeed be a reliable cue to female reproductive history (with lower WHRs indicating lower number of children). Previous studies showed such a relationship for modern and industrialized populations, but it has not been investigated in natural fertility, indigenous, more energy constrained populations facing greater trade-offs in energy allocation than do modern societies. Our sample comprised 925 women aged 13 to 95 years from seven non-industrial societies including tribes from Sub-Saharan Africa (Hadza, Datoga, and Isanzu), Western Siberia (Ob Ugric people: Khanty and Mansi), South America (Tsimane) and South Asia (Minahasans and Sangirese). We demonstrated a culturally stable, significant relationship between number of children and WHR among women, controlling for BMI and age. Based on these data, we suggest that WHR is a reliable cue to female reproductive history, and we discuss our results in the context of previous studies indicating usefulness of WHR as an indicator of health and fertility.

Added: Feb 19, 2018
Article
Saritas O., Proskuryakova L. N. Foresight. 2017. Vol. 19. No. 2. P. 152-173.

Purpose  

This paper focuses on the long-term situation with water resources, and water sector in particular, analyzed through a Foresight study. The authors attribute particular attention to implication for Russia, which is relatively better positioned regarding the availability of water resources. However, the country still faces challenges related to the protection of water resources, drinking water supply, water networks, consumption patterns, water discharge, treatment and re-use. The present study aims at identification and analysis of trends, factors and uncertainties in water supply, demand, use and re-use with a particular focus on sustainability of water systems; water use by households and industry; and new water services and products.

Design/methodology/approach  

Research methodology in this paper involves a horizon scanning exercise for the identification of the key trends, factors and uncertainties along with the identification of weak signals of future emerging trends and wild cards in the form of future surprises, shocks and other unexpected events that may disrupt the preservation of water resources and the future of the water sector. Trends characterize broad parameters for shifts in attitudes, climate, policies and business focus over periods of several years that usually have global reach. These are usually experienced by everyone and often in similar contexts. Trends may represent threats, opportunities or a mixture of them, identified through underlying processes, possible events and other future developments.

Findings  

A key systemic restriction of water use for the next decades both globally and in Russia relates to competition between agriculture, energy, manufacturing and household water use. Given that the amount of renewable water resources is almost fixed and even decreases because of pollution, circular economy solutions for water use will be required. Implications of the global trends identified in the study for Russia are dependent on the overall situation with water resources in the country. Russia has sufficient water supply: the overall intake of water for drinking and economic purposes in Russia amounts to 3 per cent of the total water resources, two-thirds of which are discarded back to water bodies. At the same time, there are substantial problems associated with the extremely uneven distribution of water resources across the country, as well as high “water intensity” of the Russian GDP. The Russian water sector is currently not very attractive for investors. Moreover, it has significantly less lobbying opportunities than other infrastructure sectors, and this complicates its institutional and financial positions. Meanwhile, there have been some positive changes with regard to activities with a short pay-off period.

Originality/value  

The paper offers one of the first studies on the future of Russian water resources with a focus on the water supply and sanitation sector. A comprehensive approach to trends identification (not found in other studies on Russian water resources) allowed authors to identify social, technological, environmental, economic, policy and value-related global trends and uncertainties. Moreover, implications of these trends and uncertainties, as well as Russia-specific trends, were outlined.

 

Added: Jan 25, 2017
Article
Tsareva O. O., Zelenyi L. M., Malova H. V. et al. Physics-Uspekhi. 2018. Vol. 61. No. 2. P. 191-202.

Earth's global magnetic field generated by an internal dynamo mechanism has been continuously changing on different time scales since its formation. Paleodata indicate that relatively long periods of evolutionary changes can be replaced by quick magnetic inversions. Based on observations, Earth's magnetic field is currently weakening and the magnetic poles are shifting, possibly indicating the beginning of the inversion process. This paper invokes Gauss coefficients to approximate the behavior of Earth's magnetic field components over the past 100 years. Using the extrapolation method, it is estimated that the magnetic dipole component will vanish by the year 3600 and at that time the geomagnetic field will be determined by a smaller value of a quadrupole magnetic component. A numerical model is constructed which allows evaluating and comparing both galactic and solar cosmic ray fluxes in Earth's magnetosphere and on its surface during periods of dipole or quadrupole domination. The role of the atmosphere in absorbing particles of cosmic rays is taken into account. An estimate of the radiation danger to humans is obtained for the ground level and for the International Space Station altitude of  km. It is shown that in the most unfavorable, minimum field interval of the inversion process, the galactic cosmic ray flux increases by no more than a factor of three, implying that the radiation danger does not exceed the maximum permissible dose. Thus, the danger of magnetic inversion periods generally should not have fatal consequences for humans and nature as a whole, despite dramatically changing the structure of Earth's magnetosphere.

Added: May 8, 2018
Article
Boulenger V., Shtyrov Y., Pulvermuller F. Neuroimage. 2012. Vol. 59. P. 3502-3513.

We investigated the time-course of cortical activation during comprehension of literal and idiomatic sentences using MEG and anatomically guided distributed source analysis. Previous fMRI work had shown that the comprehension of sentences including action-related words elicits somatotopic semantic activation along the motor strip, reflecting meaning aspects of constituent words. Furthermore, idioms more strongly activated temporal pole and prefrontal cortex than literal sentences. Here we show that, compared to literal sentences, processing of idioms in a silent reading task modulates anterior fronto-temporal activity very early-on, already 150-250 ms after the sentences' critical disambiguating words ("kick the habit"). In parallel, the meaning of action words embedded in sentences is reflected by somatotopic activation of precentral motor systems. As neural reflections of constituent parts of idiomatic sentences are manifest at the same early latencies as brain indexes of idiomatic vs. literal meaning processing, we suggest that within ¼ of a second, compositional and abstract context-driven semantic processes in parallel contribute to the understanding of idiom meaning.

Added: Oct 23, 2014
Article
Shtyrov Y., Stroganova T. Frontiers in Human Neuroscience. 2015. Vol. 9. No. 576.

This opinion responds to the commentary by Papeo and Caramazza (2014).

Added: Oct 23, 2015