Hengzongshu/ArticleAgent huggingface dataset:
Introduction: Tumor necrosis factor (TNFα) is an important proinflammatory cytokine in rheumatoid arthritis (RA) immune processes. However, TNFα activity and functions may be regulated by soluble receptors, which act as decoys, and by number, density, and co-expression of its membrane-bound receptors type 1 and 2 (TNFR1 and TNFR2). The aim of this study was to reveal associations between TNFR1/2 co-expression profile parameters and RA disease activity indicators. Methods: PBMC were analyzed from 46 healthy donors and 64 patients with RA using flow cytometry. Patients were divided according to the disease activity score (DAS) 28 index into groups with high (n = 22, 34.4%), moderate (n = 30, 46.9%), and low (n = 12, 18.8%) disease activity. Co-expression of TNFR1 and TNFR2 was studied by evaluating the percentage of cells, with different receptors, and by counting the number of receptors of each type per cell, using QuantiBritePE beads. Associations between disease severity and activity indicators and parameters of TNFα receptor expression in subpopulations of immune cells were studied. Results: T cell subsets from RA patients were characterized by co-expression of TNFR1 and TNFR2, and were found to differ significantly compared with healthy donors. Memory cells both among T helper cells and cytotoxic T cells demonstrated the most significant differences in TNFR-expression profile. Multivariable logistic regression revealed model to identified RA patients from healthy individual based on the TNFR1/2 co-expression parameters. Conclusion: The profile of TNFR1\2 co-expression differs in RA comparing with health. Proportion of TNFR1+TNFR2- cells increased significantly among memory T helper cells and activated cytotoxic T cells, and decreased significantly among naïve cytotoxic T cells and T regulatory cells as compared with health. The parameters of TNFR1\2 co-expression in RA are associated with clinical and laboratory indicators of disease activity.
One of the crucial elements contributing to the adaptation of organisms to unfavorable environmental conditions is the reaction of stress. The study of its genetic control and role in adaptation to unfavorable conditions are of special interest. The juvenile hormone (JH) acts as a gonadotropic hormone in adult insects controlling the development of the ovaries, inducing vitellogenesis and oviposition. It was shown that a decrease in JH degradation in individuals reacting to adverse conditions by stress reaction (R­individuals) causes delay in egg laying and seems to allow the population to “wait out” the unfavorable conditions, thereby contributing to the adaptation at the population level. However, monitoring natural populations of D. melanogaster for the capability of stress reaction demonstrated that they have a high percentage of individuals incapable of it (NR­individuals). The study of reproductive characteristics of R­ and NR­individuals showed that under normal conditions R­individuals have the advantage of procreating oﬀspring. Under unfavorable conditions, if the stressor is intense enough, NR­individuals die, but if its intensity is low, then they, unlike R­individuals, continue to produce oﬀspring. Based on these data, it was hypothesized that the balance of R­ and NR­alleles in the population ensures its adaptation under frequent stresses of low intensity. To verify the hypothesis by an experiment, the ftness characteristics (lifespan, fecundity) of the R and NR lines of D. virilis were studied under normal conditions and under regular heat stress of various frequency.
Measured values of the tensor analyzing power T20 for the coherent photoproduction of a π0-meson on a deuteron are analyzed in the region of large momentum transfer. The incident photons of the photoproduction reaction γd→dπ0 are the quasi-real virtual photons arising from the electron scattering in the electroproduction reaction ed→edπ0. The kinematic region of large momentum transfer is of particular interest, as it corresponds to small inter-nucleon distances in the deuteron. In this case, the amplitude of the process under study is noticeably sensitive to both the deuteron wave function at small inter-nucleon distances and the various model uncertainties arising from the description of the process for large momentum transfer. A comparison shows a significant discrepancy between the experimental data and the predictions from a number of theoretical models.
A series of lanthanide and yttrium MOFs of two structural types [M2(H2O)2(nmp)2(pzc)3] (1M) and [M2(H2O)4(pzc)3]·NMP·5H2O (2M) (where M - lanthanide or yttrium cation, nmp - N-methyl-2-pyrrolidone, pzc2- - 2,5-pyrazinedicarboxylate) was synthesized and characterized by single crystal and powder X-ray diffraction crystallography, TG, elemental analyses and IR-spectroscopy.

The effect of lanthanide contraction has led to the fact that lanthanides at the beginning of the series (from lanthanum to gadolinium) have a structure different from the structure of lanthanides at the end of the series and yttrium (from terbium and beyond). According to PXRD patterns of the obtained samples mixed metal materials could be obtained not only as crystalline mixtures of two structure types but also as crystalline products of single structure type.

Varying the ratio of lanthanides in the initial reaction mixture allowed us to obtain a wide color range of luminescence, including several near-white-light emitting samples.
A low intensity light beam emerges from a graded-index, highly multimode optical fibre with a speckled shape, while at higher intensity the Kerr nonlinearity may induce a spontaneous spatial self-cleaning of the beam. Here, we reveal that we can generate two self-cleaned beams with a mutual coherence large enough to produce a clear stable fringe pattern at the output of a nonlinear interferometer. The two beams are pumped by the same input laser, yet are self-cleaned into independent multimode fibres. We thus prove that the self-cleaning mechanism preserves the beams' mutual coherence via a noise-free parametric process. While directly related to the initial pump coherence, the emergence of nonlinear spatial coherence is achieved without additional noise, even for self-cleaning obtained on different modes, and in spite of the fibre structural disorder originating from intrinsic imperfections or external perturbations. Our discovery may impact theoretical approaches on wave condensation, and open new opportunities for coherent beam combining.
Integrative bioinformatics approaches serve as background for Next-Generation Sequencing-driven analysis for gene regulation studies [1,2].This issue of the Journal of Integrative Bioinformatics presents recent work discussed at the BGRS\SB-2020 (Bioinformatics of Genome Regulation and Structure\Systems Biology) conference held in Novosibirsk, Russia (https://bgrssb.icgbio.ru/2020/).Here we collated a number of cancer gene expression studies [3,4], as well as database development reports [5,6].The BGRS conference series on bioinformatics proceeds annually since 1998 under the joint steerage of the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences and Novosibirsk State University [7,8].Overall focus of the conference was on the analysis of gene expression regulation in a genome on systems levelsuch as gene networks and systems biology models [9].The authors were co-organizers of BGRS meetings and later satellite society meetings on bioinformatics, such as Russian-German Virtual Bioinformatics Network, Sino-Russian workshops on bioinformatics [10] (http://www.zjbioinformatics.org/meetings/2020/index.html; http://glab.hzau.edu.cn/BioInfo/index.html).
Two structures are observed close to the kinematic threshold in the Ξ0bπ− mass spectrum in a sample of proton-proton collision data, corresponding to an integrated luminosity of 3.0 fb−1, recorded by the LHCb experiment. In the quark model, two baryonic resonances with quark content bds are expected in this mass region: the spin-parity JP=(1/2)+ and JP=(3/2)+ states, denoted Ξ'−b and Ξ*−b. Interpreting the structures as these resonances, we measure the mass differences and the width of the heavier state to be m(Ξ'−b)−m(Ξ0b)−m(π−)=3.653±0.018±0.006 MeV/c2, m(Ξ*−b)−m(Ξ0b)−m(π−)=23.96±0.12±0.06 MeV/c2, Γ(Ξ*−b)=1.65±0.31±0.10 MeV, where the first and second uncertainties are statistical and systematic, respectively. The width of the lighter state is consistent with zero, and we place an upper limit of Γ(Ξ'−b)<0.08 MeV at 95% confidence level. Relative production rates of these states are also reported.Received 18 November 2014DOI:https://doi.org/10.1103/PhysRevLett.114.062004This article is available under the terms of the Creative Commons Attribution 3.0 License. Further distribution of this work must maintain attribution to the author(s) and the published article's title, journal citation, and DOI.© 2015 CERN, for the LHCb Collaboration
With the advent of the new genome editing tool of target-specifically customizable endonucleases, a huge variety of novel opportunities have become feasible. The crop improvement is one of the main applications of genome editing in plant science and plant biotechnology. The amount of publications referring to genome editing and CRISPR/Cas system based molecular tools application in crops is permanently growing.

The aim of this study is the systematization and cataloging of these data. Earlier we published the first catalog of targeted crop genome modifications as of February 10, 2017. The current review is an update of the catalog; it covers research papers on crop genome modifications from February 10, 2017 to August 17, 2018, found by searching 47 crop names in the Scopus database.

Over one year and a half, 377 articles mentioning CRISPR/Cas and crop names have been published, of which 131 articles describe an experimental application of this tool for editing 193 genes in 19 crops, including rice with the largest number of genes modified (109 genes). Editing 50 of 193 genes was aimed at crop improvement. The catalog presented here includes these 50 genes, specifying the cultivars, each gene and gene product function, modification type and delivery method used. The current full list of genes modified with CRISPR/Cas with the aim of crop improvement is 81 in 16 crops (for 5 years from August 2013 to August 2018). In this paper, we also summarize data on different modifications types in different crops and provide a brief review of some novel methods and approaches that have appeared in crop genome editing research over the reviewed period. Taken together, these data provide a clear view on current progress in crop genome modifications and traits improvement using CRISPR/Cas based genome editing technology.
The concept of informativeness of nonlinear plasma physics scenarios is explained. Natural ideas of developing highly informative models of plasma kinetics are spelled out.

A maximally informative version of inelastic scattering of electromagnetic waves by Langmuir waves in a weakly turbulent inhomogeneous plasma is developed with consideration of possible changes in wave polarization. In addition, a new formula for wave drift in spatial positions and wave vectors is derived.

New scenarios of the respective wave drift and inelastic scattering are compared with the previous visions. The results indicate the need for further revision of the traditional understanding of nonlinear plasma phenomena.
Direct numerical modeling of the effect of the local area of energy release on the development of the combustion propagation process in a high-speed flow of a homogeneous fuel-air mixture (H2+air) has been carried out. The mathematical model of the energy source describes the physical phenomena characteristic of pulsed energy supply using laser radiation. Energy supply and ignition are simulated taking into account a given kinetic scheme. The results on the space-time evolution of the ignition region are presented. The dependence of the position of the ignition region on the speed of the oncoming flow has been investigated.
For a long time discoveries were recognized only in natural sciences. We can talk about 'discoveries' in the social sciences only in some other sense. At the same time the accumulation of general theoretical knowledge in economics and sociology is not in doubt.

Eleven criteria of 'positive knowledge' (respectively, 'discoveries' when such knowledge is first acquired) are formulated. Three groups of scientific and philosophical disciplines with similar indicators according to these criteria are distinguished. To solve this difficulty the metaphor of 'a lock' (obstacles to cognition), 'a key' (intellectual means selected and created to obtain reliable knowledge) and 'a view' (holistic meaningful image on 'opening different doors') was used.

In philosophy (with the exception of logic and analytical philosophy) it is difficult to talk about discoveries and knowledge due to the lack of agreement regarding any non-trivial judgments with a philosophical level of generality and abstractness. At the same time the development of philosophy is more than the accumulation of ideas as optional opinions. Even if philosophy does not produce full-fledged discoveries and generally accepted knowledge it progressively develops its ideas as heuristic 'keys' for scientific research and as 'views' that generalize heterogeneous, accumulated scientific knowledge connecting them with changing self-consciousness and values in human generations.
Two new isostructural phases Fe7N3-C2/m and Fe7C3-C2/m which are dynamically and thermodynamically stable under the Earth's core conditions were predicted.

We carried out ab initio calculations on the crystal structure prediction and determination of P-T diagrams within the quasi-harmonic approximation for Fe7N3 and Fe7C3.

The Fe7C3-C2/m phase stabilizes preferentially to the known h-Fe7C3 at 253-344 GPa in the temperature range of 0-5000 K, and the Fe7N3-C2/m stabilizes preferentially relative to the β-Fe7N3 - at ∼305 GPa over the entire temperature range. This indicate that carbon and nitrogen can mutually coexist and replace each other in the Earth's and other planetary cores similarly to low pressure phases of the same compounds.
The TiO2 photocatalyst doped with nitrogen was synthesized via a precipitation method and investigated in the oxidation of acetone vapor under UV (371 nm) and visible light (450 nm).

The data were collected in a continuous-flow set-up equipped with a long-path IR gas cell for in situ analysis of oxidation products and evaluation of the photocatalytic activity. The IR spectra for inlet and outlet reaction mixtures and their change during the process are presented. A technique for quantitative analysis of initial substrate and oxidation product using collected IR spectra is described. The effects of main operational parameters, namely, outlet concentration of oxidizing substrate in the range of 0–25 μmol/L, humidity in the range of 10–85%, and surface density of photocatalyst in the range of 0.6–5.7 mg/cm2 were investigated, and the data received are presented.

The data show the influence of these parameters on the UV and visible light photocatalytic activity of N-doped TiO2. The data is publicly available on GitHub according to the link: https://github.com/1kovalevskiy/Effect-of-the-operational-parameters.
Using the density matrix formalism

we prove the existence of the periodic steady-state for an arbitrary periodically driven system described by linear dynamic equations

The presented derivation simultaneously contains a simple and effective computational algorithm, which automatically guarantees a full account of all frequency components
Klyuchevskoy and surrounding volcanoes in central Kamchatka form the Northern Group of Volcanoes (NGV), which is an area of particularly diverse and intensive Pleistocene‐Holocene volcanism. In this study, we present a new seismic tomographic model of the crust and uppermost mantle beneath NGV based on local earthquake data recorded by several permanent and temporary seismic networks including a large‐scale experiment that was conducted in 2015–2016 by an international scientific consortium. Having an unprecedented resolution for this part of Kamchatka, the new model reveals many features associated with the present and past volcanic activity within the NGV. In the upper crust, we found several prominent high‐velocity anomalies interpreted as traces of large basaltic shield volcanoes, which were hidden by more recent volcanic structures and sediments. We interpret the mantle structure to reflect asthenospheric flow up through a slab window below the Kamchatka‐Aleutian junction that feeds the entire NGV. The interaction of the hot asthenospheric material with fluids released from the slab determines the particular volcanic activity within the NGV. We argue that the eastern branch of the Central Kamchatka Depression, which is associated with a prominent low‐velocity anomaly in the uppermost mantle, was formed as a recent rift zone separating the NGV from the Kamchatka Eastern Ranges.
Novosibirsk Scientific Center (NSC), also known worldwide as Akademgorodok, is one of the largest Russian scientific centers hosting Novosibirsk State University (NSU) and more than 35 research organizations of the Siberian Branch of Russian Academy of Sciences including Budker Institute of Nuclear Physics (BINP), Institute of Computational Technologies, and Institute of Computational Mathematics and Mathematical Geophysics (ICM&MG). Since each institute has specific requirements on the architecture of computing farms involved in its research field, currently we've got several computing facilities hosted by NSC institutes, each optimized for a particular set of tasks, of which the largest are the NSU Supercomputer Center, Siberian Supercomputer Center (ICM&MG), and a Grid Computing Facility of BINP.

A dedicated optical network with the initial bandwidth of 10 Gb/s connecting these three facilities was built in order to make it possible to share the computing resources among the research communities, thus increasing the efficiency of operating the existing computing facilities and offering a common platform for building the computing infrastructure for future scientific projects. Unification of the computing infrastructure is achieved by extensive use of virtualization technology based on XEN and KVM platforms.

This contribution gives a thorough review of the present status and future development prospects for the NSC virtualized computing infrastructure and the experience gained while using it for running production data analysis jobs related to HEP experiments being carried out at BINP, especially the KEDR detector experiment at the VEPP-4M electron-positron collider.
Using high-speed video recording and the method of dual laser scanning the gas-liquid flow was investigated in a rectangular microchannel with an aspect ratio of 0.74 (cross section 269×362 μm). The T-mixer was used at the channel's inlet for the two-phase flow formation.

The peculiarity of this work is using a number of liquids (ethanol, distilled water, 40% aqueous ethanol) with different physical properties, including surface tension, viscosity, and density, with nitrogen. Experiments were carried out for the vertically upward and horizontal flow.

Using laser scanning method the maps of flow patterns were obtained for all mixtures.
In this paper, we study stratified flows and internal waves in the fracture zones of the Mid Atlantic Ridge. The results of measurements carried out in the 39th and 40th cruises of RV Akademik Sergey Vavilov in the autumn of 2014 and 2015 are presented. Hydrophysical properties of the near-bottom flows are studied experimentally on the basis of CTD- and LADCP profiling. Theoretical analysis involves mathematical formulation of stratified fluid flow which uses CTD-data obtained from field observation in the Vema Fracture Zone region. Spectral properties and kinematic characteristics of internal waves are calculated by finite element method.
L’article analyse le niveau de maitrise du français tel qu’il est manifesté dans les cahiers intimes d’une princesse russe, écrits en français entre 1830 et 1848. Nous analyserons tout d’abord les marques transcodiques typiques du code switching et leur fonctionnement dans le texte, puis les erreurs de langage relevées dans les 5 cahiers analysés, qui représentent plus de 1000 pages manuscrites. Nous arriverons à la conclusion que le niveau de langue de la diariste et de son entourage était très élevé, très faiblement marqué par des interférences avec la langue maternelle.
An algorithm is described for tagging the flavour content at production of neutral B mesons in the LHCb experiment.

The algorithm exploits the correlation of the flavour of a B meson with the charge of a reconstructed secondary charm hadron from the decay of the other b hadron produced in the proton-proton collision. Charm hadron candidates are identified in a number of fully or partially reconstructed Cabibbo-favoured decay modes. The algorithm is calibrated on the self-tagged decay modes B+ → J/ψ K+ and B0 → J/ψ K*0 using 3.0 fb−1 of data collected by the LHCb experiment at pp centre-of-mass energies of 7 TeV and 8 TeV.

Its tagging power on these samples of B → J/ψ X decays is (0.30 ± 0.01 ± 0.01)%.
As urogenital tuberculosis (UGTB) has no specific clinical features, it is often overlooked.

To identify some of the reasons for misdiagnosing UGTB we performed a systematic review. We searched in Medline/PubMed papers with keywords 'urogenital tuberculosis, rare' and 'urogenital tuberculosis, unusual'. 'Urogenital tuberculosis, rare' presented 230 articles and 'urogenital tuberculosis, unusual' presented 81 articles only, a total of 311 papers. A total of 34 papers were duplicated and so were excluded from the review. In addition, we excluded from the analysis 33 papers on epidemiological studies and literature reviews, papers describing non-TB cases and cases of TB another than urogenital organs (48 articles), cases of congenital TB (three articles), UGTB as a case of concomitant disease (16 articles), and UGTB as a complication of BCG-therapy (eight articles). We also excluded 22 articles dedicated to complications of the therapy, which made a total of 164 articles. Among the remaining 147 articles we selected 43 which described really unusual, difficult to diagnose cases. We also included in our review a WHO report from 2014, and one scientific monograph on TB urology.

The most frequent reasons for delayed diagnosis were absence typical clinical features of UGTB, and the tendency of UGTB to hide behind the mask of another disease. We can conclude that actually UGTB is not rare disease, but it is often an overlooked disease. The main reasons for delayed diagnosis are vague, atypical clinical features and a low index of suspicion.