Hengzongshu/ArticleAgent huggingface dataset:
Identification of microorganisms by MALDI-TOF mass spectrometry is a very efficient method with high throughput, speed, and accuracy. However, it is significantly limited by the absence of a universal database of reference mass spectra. This problem can be solved by creating an Internet platform for open databases of protein spectra of microorganisms. Choosing the optimal mathematical apparatus is the pivotal issue for this task. In our previous study we proposed the geometric approach for processing mass spectrometry data, which represented a mass spectrum as a vector in a multidimensional Euclidean space. This algorithm was implemented in a Jacob4 stand-alone package. We demonstrated its efficiency in delimiting two closely related species of the Bacillus pumilus group. In this study, the geometric approach was realized as R scripts which allowed us to design a Web-based application. We also studied the possibility of using full spectra analysis (FSA) without calculating mass peaks (PPA), which is the logical development of the method. We used 74 microbial strains from the collections of ICiG SB RAS, UNIQEM, IEGM, KMM, and VGM as the models. We demonstrated that the algorithms based on peak-picking and analysis of complete data have accuracy no less than that of Biotyper 3.1 software. We proposed a method for calculating cut-off thresholds based on averaged intraspecific distances. The resulting database, raw data, and the set of R scripts are available online at https://icg-test.mydisk.nsc.ru/s/qj6cfZg57g6qwzN .
Reactions of [VCl3(thf)3] or VBr3 with 2,2′-bipyridine (bpy) or 1,10-phenanthroline (phen) in a 1:1 molar ratio in air under solventothermal conditions has afforded polymeric oxidovanadium(IV) four complexes 1–4 of a general formula [VO(L)X2]n (L = bpy, phen and X = Cl, Br). Monomeric complex [VO(DMF)(phen)Br2] (4a) has been obtained by the treatment of compound 4 with DMF.

The complexes were characterized by IR spectroscopy and elemental analysis. The crystal structures of 3 and 4a were determined by an X-ray diffraction (XRD) analysis. The {VOBr2(bpy)} fragments in 3 form infinite chains due to the V = O…V interactions. The vanadium atom has a distorted octahedral coordination environment. Complexes 1–4 have been tested as catalysts in the homogeneous oxidation of alkanes (to produce corresponding alkyl hydroperoxides which can be easily reduced to alcohols by PPh3) and alcohols (to corresponding ketones) with H2O2 or tert-butyl hydroperoxoxide in MeCN.

Compound 1 exhibited the highest activity. The mechanism of alkane oxidation was established using experimental selectivity and kinetic data and theoretical DFT calculations. The mechanism is of the Fenton type involving the generation of HO• radicals.
The reported activity aims at validating the operation of sorption STES in various cold climatic zones in Europe. Accordingly, the reference boundary conditions were identified by means of a climatic analysis in two climatic zones, namely, Central and Northern Europe.

In this study, the development and characterization of composite sorbents based on commercial mesoporous silica gels and LiCl for seasonal thermal energy storage (STES) applications is described. The acquired mesoporous silica gels were characterized, to evaluate the textural properties, i.e. specific pore volume and pore size, needed to define the optimal salt solution compositions to maximize the amount of salt embedded. The synthesized samples were firstly investigated using scanning electron microscopy and nitrogen physisorption that demonstrate the presence of a small quantity of salt over the external surface rather than inside the pores. A hydrothermal treatment, based on slow adsorption followed by a slow desorption step, was defined to solve this issue.

Finally, starting from the measured equilibrium isobars, the expected STES density at material level was evaluated, obtaining values as high as 1080 J/g under cold Northern European climatic condition, corresponding to 650 MJ/m3.
The Mongolian-Siberian species Deracantha onos (2n = 29, NF = 31) is characterized by an extensive amount of C-heterochromatin occurring on the M2 chromosomes as a large interstitial C-block and on M6, S8, S9, and S10 chromosomes as large distal C-bands.
We consider two basic nuclear reactions: capture of neutrons by protons, n + p → γ + d, and its time-reversed counterpart, photodisintegration of the deuteron, γ + d → n + p. In both of these cases we assume that the incoming beam of neutrons or photons is 'twisted' by having an azimuthal phase dependence, i.e., it carries an additional angular momentum along its direction of propagation. Taking a low-energy limit of these reactions, we derive relations between corresponding transition amplitudes and cross sections with plane-wave beams and twisted beams. Implications for experiments with twisted cold neutrons and twisted photon beams are discussed.
The goldthread genus Coptis includes 15 species disjunctly distributed in eastern Asia and North America. Here, we provide a dated phylogeny for the genus with all 15 species. Our results indicate that Coptis contains two strongly supported clades (I and II). Clade I consists of subg. Coptis and sect. Japonocoptis of subg. Metacoptis; clade II composes sect. Japonocoptis of subg. Metacoptis. Central leaflet base, sepal shape, and petal blade carry a strong phylogenetic signal in Coptis, while leaf type, sepal and petal color, and petal shape exhibit relatively higher levels of evolutionary flexibility. Our dating and biogeographic analyses indicate that a vicariance event between Japan-North America occurred in the middle Miocene, resulting in the split of Coptis and its sister group. Subsequently, a colonization event occurred at 9.55 Ma from Japan to mainland China. Both vicariance and dispersal events have played important roles in shaping the current distribution and endemism of Coptis, likely resulting from eustatic sea-level changes, mountain formation processes and an increasing drier and cooler climate from the middle Miocene onwards.
The kinetics and the mechanism of thermal decomposition of ultrahigh-molecular-weight polyethylene without additive and with TPP additives in oxidative and inert media has been studied using the method of differential mass-spectrometric thermal analysis at a high heating rate and the method of thermogravimetric analysis at a low heating rate, aimed at understanding the mechanism of reducing combustibility of UHMWPE with TPP additives. The results of the study may testify to the fact that not the thermal polymer degradation reactions but the gas-phase reactions in the UHMWPE flame with TPP participation are responsible for flame retardancy of UHMWPE.
Background: Previous studies of co-expression profile of receptors to tumor necrosis factor alpha (TNF) in rheumatoid arthritis (RA) have revealed a number of indicators associated with diseases activity with 93% sensitivity and 90% specificity. However, the ratio of receptors to cytokines remains poorly understood. However, the question of therapy effect and its effectiveness in various alteration of cytokine receptors balance remains under investigated. Objectives: To evaluate the dynamics of co-expression and quantitative expression of type 1 and 2 receptors for TNF in the subpopulations of CD3+CD8+ cells associated with changes in disease severity before and after effective basic therapy. Methods: Subanalysis of patients with high disease activity level successfully treated with methotrexate and oral glucocorticoids (n = 9) was performed. As a control group, we used data from 43 healthy donors, comparable by sex and age distribution. Subpopulations of cytotoxic T cells were studied, which were included in the final diagnostic models for differentiating different degrees of severity of RA: naive T cells and memory T cells. The dynamics of changes in the indicators of receptors number and proportion of cells expressing the corresponding receptor were compared. Results: For naïve cytotoxic T cells, the main revealed feature was the relative stability of the number of expressed receptors (both TNFR1 and TNFR2), regardless of the therapy, while this number did not significantly differ from healthy ones for TNFR1 and was significantly lower for TNFR2 (p <0.05 for all three fractions). At the same time, in terms of cell percentage, on the contrary, the therapy led to a change in total proportion of TNFR1 + cells closer to healthy donors indicators, and the proportion of TNFR2 + cells in the opposite direction. For cytotoxic T memory cells, it was demonstrated that after successful treatment a significant increase in the number of type 1 receptors was observed, with a decrease in TNFR1+ cells proportion, while these indicators were close to the values of healthy donors. At the same time, healthy donors were characterized by a significantly higher expression of type 2 receptors in terms of cell density of receptors. It is noteworthy that with successful therapy, a slight increase in the number of TNFR2 was observed with a sharp decrease in the proportion of TNFR2+ cells (p = 0.043). Conclusion: The balance of TNF receptor expression on cells actively involved in immunopathological processes affects both the density distribution of receptors on cells and co-expression in a subpopulation. Effective treatment of RA leads to equalization of the expression profile either by the percentage of cells or by the number of receptors, approaching the indicators of healthy donors, but not simultaneously. Disclosure of Interests: None declared
The first observation of the B¯0→J/ψK+K− decay is presented with a data sample corresponding to an integrated luminosity of 1.0 fb−1 of pp collisions at a center-of-mass energy of 7 TeV collected with the LHCb detector.

An amplitude analysis of the final state in the B¯0→J/ψK+K− decay is performed to separate resonant and nonresonant contributions in the K+K− spectrum.

The branching fraction is measured to be B(B¯0→J/ψK+K−)=(2.53±0.31±0.19)×10−6, where the first uncertainty is statistical and the second is systematic. Evidence of the a0(980) resonance is reported with statistical significance of 3.9 standard deviations. The corresponding product branching fraction is measured to be B(B¯0→J/ψa0(980),a0(980)→K+K−)=(4.70±3.31±0.72)×10−7, yielding an upper limit of B(B¯0→J/ψa0(980),a0(980)→K+K−)<9.0×10−7 at 90% confidence level. No evidence of the resonant decay B¯0→J/ψϕ is found, and an upper limit on its branching fraction is set to be B(B¯0→J/ψϕ)<1.9×10−7 at 90% confidence level.
Novel alternatives to traditional antibiotics are now of great demand for the successful treatment of microbial infections.

Here, we present the engineering and properties of new oligonucleotide inhibitors of RNase P, an essential bacterial enzyme. The series of 2'-O-methyl RNA (2'-OMe-RNA) and phosphoryl guanidine oligonucleotides were targeted to the substrate-binding region of M1 RNA subunit of the RNase P.

Uniformly modified 2'-OMe RNA and selectively modified phosphoryl guanidine oligonucleotides possessed good stability in biological media and effectively inhibited RNase P. Their conjugates with transporting peptides were shown to penetrate bacterial cells (Escherichia coli and Acinetobacter baumannii) and inhibit bacterial growth.
For a signed cyclic graph [Formula: see text], we can construct a unique virtual link [Formula: see text] by taking the medial construction and converting 4-valent vertices of the medial graph to crossings according to the signs. If a virtual link can occur in this way then we say that the virtual link is graphical.

In this paper, we shall prove that a virtual link [Formula: see text] is graphical if and only if it is checkerboard colorable. On the other hand, we introduce a polynomial [Formula: see text] for signed cyclic graphs, which is defined via a deletion-marking recursion. We shall establish the relationship between [Formula: see text] of a signed cyclic graph [Formula: see text] and the bracket polynomial of one of the virtual link diagrams associated with [Formula: see text].

Finally, we give a spanning subgraph expansion for [Formula: see text].
ЭКСПЕРИМЕНТАЛЬНОЕ ОБОСНОВАНИЕ ПРИМЕНЕНИЯ ПЕРОРАЛЬНОГО ТРОМБОЛИТИКА НА ОСНОВЕ ИММОБИЛИЗИРОВАННЫХ СУБТИЛИЗИНОВ И АНТИКОАГУЛЯНТА НА ОСНОВЕ НИЗКОМОЛЕКУЛЯРНОГО ГЕПАРИНА ДЛЯ ЛЕЧЕНИЯ ТРОМБОЗА СОСУДОВ ЛЕГКИХ
Breast cancer is the leading cause of cancer death in women worldwide due to the complicated etiology involving both genetic and environmental factors.

BC was induced by N -Methyl- N -Nitrosourea administration intermammary in Wistar female. Studied frequency of development of NMU-induced BC, phenotype of BC cells, phenotype of MSC from mammary gland tissue, quantity and quality of immunocompetent cells, expression of miRNAs, hormone levels and cytokines were done for estimate sensitivity to chemotherapy.

We showed that MNU-induced BC developed in 90%, immunohistochemical similar to human luminal A type of BC with higher proliferation activity. We estimated significantly increased count of BC-MSC with CD45+CD90-, and CD45+CD90+, and CD45-CD90+ phenotype in animal with MNU-induced BC. Chemotherapy caused changes in quality and quantity of immunocompetent cells, decrease of prolactin and luteinizing hormone levels, and some changes in expression of pro-oncogenic or tumor-suppressing miRNAs. In MNU-induced BC animal were observed increased serum levels of pro-inflammatory cytokines. In regional lymph nodes found increased count of macrophages and presence of tumor cells. Intermammary administration of NMU possessed to breast cancer development with similarities to human luminal B phenotype. This MNU-induced breast cancer may serve as a model to study efficiency of chemotherapy.
Recovery of optical phases using direct intensity detection methods is an ill-posed problem and some prior information is required to regularize it. In the case of multi-mode fibers, the known structure of eigenmodes is used to recover optical field and find mode decomposition by measuring intensity distribution. Here we demonstrate numerically and experimentally a mode decomposition technique that outperforms the fastest previously published method in terms of the number of modes while showing the same decomposition speed. This technique improves signal-to-noise ratio by 10 dB for a 3-mode fiber and by 7.5 dB for a 5-mode fiber.
Tissue protection from oxidative stress by antioxidants is of vital importance for cellular metabolism.

The lens mostly consists of fiber cells lacking nuclei and organelles, having minimal metabolic activity; therefore, the defense of the lens tissue from the oxidative stress strongly relies on metabolites. Protein-free extracts from lenses and gills of freshwater fish,
оценка ЭФФекТиВноСТи СоВРеМеннЫХ МеТодоВ коРРекции иСТМико-цеРВикалЬноЙ недоСТаТоЧноСТи 1
Nuclear magnetic resonance (NMR) is a noninvasive and nondestructive tool able to access several observable quantities in biofilms such as chemical composition, diffusion, and macroscale structure and transport.

Pulsed gradient spin echo (PGSE) NMR techniques were used to measure spectrally resolved biomacromolecular diffusion in biofilm biomass, extending previous research on spectrally resolved diffusion in biofilms. The dominant free water signal was nulled using an inversion recovery modification of the traditional PGSE technique in which the signal from free water is minimized in order to view the spectra of components such as the rotationally mobile carbohydrates, DNA, and proteins.

Diffusion data for the major constituents obtained from each of these spectral peaks demonstrate that the biomass of the biofilm contains both a fast and slow diffusion component. The dependence of diffusion on antimicrobial and environmental challenges suggests the polymer molecular dynamics measured by NMR are a sensitive indicator of biofilm function.
Territory of Mongolia is situated in the center of Asia, a crossroad of the potential migration routes, that connect different Eurasian macroregions. Here an example of earliest appearance and longterm existence of small blade and microblade production has been found. Beyond that, the industries, that appeared within limited area of the Middle Selenga Basin in the late MIS3 — early MIS2, contained the earliest for Northern and Central Asia geometric and non-geometric microliths. They have been found in the sediments of Kharganyn Gol 5 and Tolbor-4, — 16 and –21. They end up in LGM — post- LGM which cause depopulation in the region and following changes in the human groups, occupying this territory. An understanding of the character, causes and specifics of such early appearance of the microblade and bladelet production, and especially geometric microliths, impose the arrangement and definition of the terminology, associated with microlithic assemblages in Asia. This is due to the fact that in the archaeological definitions of both processes and the desired forms of artifacts associated with the production and use of microliths, there are significant discrepancies that complicate the understanding of the described phenomena. The article provides an overview of the research terminology of microlithization processes, and also determines the position of the microlithic complexes of Mongolia in the Upper Paleolithic system of the eastern part of Asia. Keywords: Mongolia, East Asia, Upper Paleolithic, lithic industries, microlithic technology
A high-precision determination of the main parameters of the \psi(2S) resonance has been performed with the KEDR detector at the VEPP-4M e^{+}e^{-} collider in three scans of the \psi(2S) -- \psi(3770) energy range. Fitting the energy dependence of the multihadron cross section in the vicinity of the \psi(2S) we obtained the mass value M = 3686.114 +- 0.007 +- 0.011 ^{+0.002}_{-0.012} MeV and the product of the electron partial width by the branching fraction into hadrons \Gamma_{ee}*B_{h} = 2.233 +- 0.015 +- 0.037 +- 0.020 keV. The third error quoted is an estimate of the model dependence of the result due to assumptions on the interference effects in the cross section of the single-photon e^{+}e^{-} annihilation to hadrons explicitly considered in this work. Implicitly, the same assumptions were employed to obtain the charmonium leptonic width and the absolute branching fractions in many experiments. Using the result presented and the world average values of the electron and hadron branching fractions, one obtains the electron partial width and the total width of the \psi(2S): \Gamma_{ee} =2.282 +- 0.015 +- 0.038 +- 0.021 keV, \Gamma = 296 +- 2 +- 8 +- 3 keV. These results are consistent with and more than two times more precise than any of the previous experiments.
Genome assemblies are in the process of becoming an increasingly important tool for understanding genetic diversity in threatened species. Unfortunately, due to limited budgets typical for the area of conservation biology, genome assemblies of threatened species, when available, tend to be highly fragmented, represented by tens of thousands of scaffolds not assigned to chromosomal locations. The recent advent of high-throughput chromosome conformation capture (Hi-C) enables more contiguous assemblies containing scaffolds spanning the length of entire chromosomes for little additional cost. These inexpensive contiguous assemblies can be generated using Hi-C scaffolding of existing short-read draft assemblies, where N50 of the draft contigs is larger than 0.1% of the estimated genome size and can greatly improve analyses and facilitate visualization of genome-wide features including distribution of genetic diversity in markers along chromosomes or chromosome-length scaffolds. We compared distribution of genetic diversity along chromosomes of eight mammalian species, including six listed as threatened by IUCN, where both draft genome assemblies and newer chromosome-level assemblies were available. The chromosome-level assemblies showed marked improvement in localization and visualization of genetic diversity, especially where the distribution of low heterozygosity across the genomes of threatened species was not uniform.
Previous studies suggest a potential link between glycosylation and prostate cancer.

To better characterize the relationship between the two, we performed a study to comprehensively evaluate the associations between genetically predicted blood plasma N-glycan levels and prostate cancer risk.Using genetic variants associated with N-glycan levels as instruments, we evaluated the associations between levels of 138 plasma N-glycans and prostate cancer risk. We analyzed data of 79,194 cases and 61,112 controls of European ancestry included in the consortia of BPC3, CAPS, CRUK, PEGASUS, and PRACTICAL.

We identified three N-glycans with genetically predicted levels in plasma to be associated with prostate cancer risk after Bonferroni correction. The estimated odds ratios (95% confidence intervals) were 1.29 (1.20-1.40), 0.80 (0.74-0.88), and 0.79 (0.72-0.87) for PGP18, PGP33, and PGP109, respectively, per every one standard deviation increase in genetically predicted levels of N-glycan. However, the instruments for these N-glycans only involved one to two variants. The proportions of variations that can be explained by the instruments range from 1.58% to 2.95% for these three N-glycans.We observed associations between genetically predicted levels of three N-glycans PGP18, PGP33, and PGP109 and prostate cancer risk. Given the correlated nature of the N-glycans and that many N-glycans share genetic loci, pleiotropy is a major concern. Future work is warranted to better characterize the relationship between N-glycans and prostate cancer.
In recent years, significant success in a plasma stabilization, heating and confinement in Gas Dynamic Trap (GDT) has been acheived. However, transition processes such as fast ions buildup, ion and electron temperature growth, etc., are still underway until the end of plasma heating. Thus, heating sources worktime (around 5 ms) is too short for plasma parameters to become stationary. In this work we propose a project of GDT-based stationary plasma experiment with pulse length long enough to finish all transition processes. The implemetation of the project will allow us to test GDT stabilization, heating and confinement methods to stationary conditions and to scale the methods to reactor-sized devices. Features of the project include a superconducting magnetic system with 15 T magnetic mirror field, 30 ms plasma pulse and mixed neutral particle and ECR heating. Results of numerical simulations of such experiment using DOL code are also presented.
A search for a heavy, CP-odd Higgs boson, A, decaying into a Z boson and a 125 GeV Higgs boson, h, with the ATLAS detector at the LHC is presented. The search uses proton–proton collision data at a centre-of-mass energy of 8 TeV corresponding to an integrated luminosity of 20.3 fb−1. Decays of CP-even h bosons to ττ or bb pairs with the Z boson decaying to electron or muon pairs are considered, as well as h→bb decays with the Z boson decaying to neutrinos. No evidence for the production of an A boson in these channels is found and the 95% confidence level upper limits derived for σ(gg→A)×BR(A→Zh)×BR(h→ff¯) are 0.098–0.013 pb for f=τ and 0.57–0.014 pb for f=b in a range of mA=220–1000GeV. The results are combined and interpreted in the context of two-Higgs-doublet models.
A precise measurement of the cross section for the process e+e−→K+K−(γ) from threshold to an energy of 5 GeV is obtained with the initial-state radiation (ISR) method using 232 fb−1 of data collected with the BABAR detector at e+e− center-of-mass energies near 10.6 GeV.

The measurement uses the effective ISR luminosity determined from the e+e−→μ+μ−(γ)γISR process with the same data set.

The corresponding lowest-order contribution to the hadronic vacuum polarization term in the muon magnetic anomaly is found to be aμKK,LO=(22.93±0.18stat±0.22syst)×10−10. The charged kaon form factor is extracted and compared to previous results. Its magnitude at large energy significantly exceeds the asymptotic QCD prediction, while the measured slope is consistent with the prediction.