Hengzongshu/ArticleAgent huggingface dataset:
The most popular model for the search of ChIP-seq data for transcription factor binding sites (TFBS) is the positional weight matrix (PWM). However, this model does not take into account dependencies between nucleotide occurrences in different site positions. Currently, two recently proposed models, BaMM and InMoDe, can do as much. However, application of these models was usually limited only to comparing their recognition accuracies with that of PWMs, while none of the analyses of the co-prediction and relative positioning of hits of different models in peaks has yet been performed.

To close this gap, we propose the pipeline called MultiDeNA. This pipeline includes stages of model training, assessing their recognition accuracy, scanning ChIP-seq peaks and their classification based on scan results. We applied our pipeline to 22 ChIP-seq datasets of TF FOXA2 and considered PWM, dinucleotide PWM (diPWM), BaMM and InMoDe models.

The combination of these four models allowed a significant increase in the fraction of recognized peaks compared to that for the sole PWM model: the increase was 26.3 %. The BaMM model provided the main contribution to the recognition of sites. Although the major fraction of predicted peaks contained TFBS of different models with coincided positions, the medians of the fraction of peaks containing the predictions of sole models were 1.08, 0.49, 4.15 and 1.73 % for PWM, diPWM, BaMM and InMoDe, respectively. Thus, FOXA2 BSs were not fully described by only a sole model, which indicates theirs heterogeneity. We assume that the BaMM model is the most successful in describing the structure of the FOXA2 BS in ChIP-seq datasets under study.
Preliminary screening in a batch reactior was performed with a series of Ru, Ir, Pt, Co, and Cu catalysts, earlier efficiently applied for levulinic acid hydrogenation to GVL.

Hydrogenation of γ-valerolactone (GVL) in polar solvents (n-butanol, 1,4-dioxane) to 1,4-pentanediol (PDO) and 2-methyltetrahydrofuran (MTHF) was performed at 363–443 K in a fixed bed reactor under overall H2 pressure of 0.7–1.3 MPa. The fresh catalysts were analyzed by transmission electron microscopy (TEM), X-ray fluorescent analysis (XRF), temperature programmed reduction by H2 (H2-TPR), and N2 physisorption. Cu/SiO2 prepared by reduction of copper hydroxosilicate with chrysocolla mineral structure provided better selectivity of 67% towards PDO at 32% GVL conversion in a continuous flow reactor. This catalyst was applied to study the effect of temperature, hydrogen pressure, and contact time.

The main reaction products were PDO, MTHF, and traces of pentanol, while no valeric acid was observed. Activity and selectivity to PDO over Cu/SiO2 did not change over 9 h, indicating a fair resistance of copper to leaching.
Triarylmethyl (trityl, TAM) based spin labels represent a promising alternative to nitroxides for EPR distance measurements in biomolecules. Herewith, we report synthesis and comparative study of series of model DNA duplexes, 5′-spin-labeled with TAMs and nitroxides. We have found that the accuracy (width) of distance distributions obtained by double electron–electron resonance (DEER/PELDOR) strongly depends on the type of radical. Replacement of both nitroxides by TAMs in the same spin-labeled duplex allows narrowing of the distance distributions by a factor of 3. Replacement of one nitroxide by TAM (orthogonal labeling) leads to a less pronounced narrowing but at the same time gains sensitivity in DEER experiment due to efficient pumping on the narrow EPR line of TAM. Distance distributions in nitroxide/nitroxide pairs are influenced by the structure of the linker: the use of a short amine-based linker improves the accuracy by a factor of 2. At the same time, a negligible dependence on the linker length is found for the distribution width in TAM/TAM pairs. Molecular dynamics calculations indicate greater conformational disorder of nitroxide labels compared to TAM ones, thus rationalizing the experimentally observed trends. Thereby, we conclude that double spin-labeling using TAMs allows obtaining narrower spin–spin distance distributions and potentially more precise distances between labeling sites compared to traditional nitroxides.
In Drosophila salivary gland polytene chromosomes, a substantial portion of heterochromatin is underreplicated. The combination of mutations SuURES and Su(var)3-906 results in the polytenization of a substantial fraction of unique and moderately repeated sequences but has almost no effect on satellite DNA replication. The Rap1 interacting factor 1 (Rif) protein is a conserved regulator of replication timing, and in Drosophila, it affects underreplication in polytene chromosomes. We compared the morphology of pericentromeric regions and labeling patterns of in situ hybridization of heterochromatin-specific DNA probes between wild-type salivary gland polytene chromosomes and the chromosomes of Rif1 mutants and SuUR Su(var)3-906 double mutants. We show that, despite general similarities, heterochromatin zones exist that are polytenized only in the Rif1 mutants, and that there are zones that are under specific control of Su(var)3-9. In the Rif1 mutants, we found additional polytenization of the largest blocks of satellite DNA (in particular, satellite 1.688 of chromosome X and simple satellites in chromosomes X and 4) as well as partial polytenization of chromosome Y. Data on pulsed incorporation of 5-ethynyl-2′-deoxyuridine (EdU) into polytene chromosomes indicated that in the Rif1 mutants, just as in the wild type, most of the heterochromatin becomes replicated during the late S phase. Nevertheless, a significantly increased number of heterochromatin replicons was noted. These results suggest that Rif1 regulates the activation probability of heterochromatic origins in the satellite DNA region.
Herein, we report on a three-component supramolecular hybrid system built from specific recognition processes involving a Dawson-type polyoxometalate (POM), [P2W18O62]6–, a cationic electron-rich cluster [Ta6Br12(H2O)6]2+, and γ-cyclodextrin (γ-CD). Such materials have been investigated using a bottom-up approach by studying the specific interactions between γ-CD and both types of inorganic units.

Their ability to interact has been investigated in the solid state by single-crystal X-ray diffraction (XRD) and in solution using multinuclear NMR methods (including DOSY, EXSY, and COSY), electrospray ionization mass and UV–vis spectroscopies, electrochemistry, and isothermal titration calorimetry experiments. Single-crystal XRD analysis reveals that POM:γ-CD constitutes a highly versatile system which gives aggregates with 1:1, 1:2, and 1:3 stoichiometry. Surprisingly, these arrangements exhibit a common feature wherein the γ-CD moiety interacts with the Dawson-type POMs through its primary face. We present also the first structural model involving an octahedral-type metallic cluster with γ-CD. XRD study reveals that the cationic [Ta6Br12(H2O)6]2+ ion is closely embedded within two γ-CD units to give a supramolecular ditopic cation, suitable to be used as a linker within extended structure. Solution study demonstrates clearly that pre-associations exist in solution, for which binding constants and thermodynamic parameters have been determined, giving preliminary arguments about the chaotropic nature of the inorganic ions.

Finally, both building blocks, i.e., the ditopic supramolecular cation {[Ta6Br12(H2O)6]@2CD}2+ and the Dawson-type anion, react together to give a three-component, well-ordered hybrid material derived either as a supramolecular hydrogel or single crystals. The solid-state structure shows an unprecedented helicoidal tubular chain resulting from the periodic alternation of POM and supramolecular cation, featuring short hydrogen-bonding contacts between the electron-poor POM and electron-rich cluster. The 1D tubular ionic polymer observed in the single crystals should make it possible to understand the long-range ordering observed within the hydrogel hybrid material. The supramolecular chemical complementarities between the γ-CD-based ditopic cation and POM open a wide scope for the design of hybrid materials that accumulate synergistic functionalities.
The result of numerical simulation of a flat channel with a back-facing step in the presence of tabs by the RANS method is presented. The Reynolds number, calculated by the step height and the average flow rate velocity, was Re = 5000. The data obtained made it possible to analyze the dynamics of interaction between the separated flow behind a tab and the region of the main separation behind a step. Tabs have the greatest influence on the area in close proximity to the step.
A search for the rare decays ${B}_{s}^{0}\ensuremath{\rightarrow}{\ensuremath{\mu}}^{+}{\ensuremath{\mu}}^{\ensuremath{-}}$ and ${B}^{0}\ensuremath{\rightarrow}{\ensuremath{\mu}}^{+}{\ensuremath{\mu}}^{\ensuremath{-}}$ is performed at the LHCb experiment. The data analyzed correspond to an integrated luminosity of $1\text{ }\text{ }{\mathrm{fb}}^{\ensuremath{-}1}$ of $pp$ collisions at a center-of-mass energy of 7 TeV and $2\text{ }\text{ }{\mathrm{fb}}^{\ensuremath{-}1}$ at 8 TeV. An excess of ${B}_{s}^{0}\ensuremath{\rightarrow}{\ensuremath{\mu}}^{+}{\ensuremath{\mu}}^{\ensuremath{-}}$ signal candidates with respect to the background expectation is seen with a significance of 4.0 standard deviations. A time-integrated branching fraction of $\mathcal{B}({B}_{s}^{0}\ensuremath{\rightarrow}{\ensuremath{\mu}}^{+}{\ensuremath{\mu}}^{\ensuremath{-}})=({2.9}_{\ensuremath{-}1.0}^{+1.1})\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}9}$ is obtained and an upper limit of $\mathcal{B}({B}^{0}\ensuremath{\rightarrow}{\ensuremath{\mu}}^{+}{\ensuremath{\mu}}^{\ensuremath{-}})<7.4\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}10}$ at 95% confidence level is set. These results are consistent with the standard model expectations.
A review of seismicity of the Altai and Sayan region in 2015 is presented. The stationary network of seismic stations included 52 stations. Compared to 2014, four new seismic stations were added in the region. Additionally, two local temporary networks including 37 temporary seismic stations operated in the region.

6206 earthquakes were recorded with a total seismic energy of 5.97•1012 J.

A brief description of the seismicity in the Chui-Kurai zone of the Altai Mountains is given.
We describe the low Mach variable-density Navier-Stokes numerical iterative solution procedure implemented in the finite-volume unstructured T-FlowS code. As the test cases we use a number of analytic manufactured solutions and Rayleigh-Taylor instability problem from the literature for algorithm verification purposes. The tests show that the code is second-order accurate in agreement with the spatial discretization scheme. We outline the recent combustion ADEF model implemented in the program.
Autophagy is a degradative process in which cellular organelles and proteins are recycled to restore homeostasis and cellular metabolism. Autophagy can be either a prosurvival or a prodeath process and remains one of the most fundamental processes for cell vitality. Thus autophagy modulation is an important approach for reinforcement anticancer therapeutics. Earlier we have demonstrated that recombinant analog of human milk protein lactaptin (RL2) induced apoptosis of various cultured cancer cells and activated lipidation of microtubule-associated protein 1 light chain 3 (LC3).

In this study we investigated whether autophagy inhibitors—chloroquine (CQ), Ku55933 (Ku), and 3-methyladenine (3MA)—or inducer—rapamycin (Rap)—can enhance cytotoxic activity of lactaptin analog in cancer cells and its anticancer activity in the mice model. Western Blot analysis revealed that RL2 induced short-term autophagy in MDA-MB-231 and MCF-7 cells at early stages of incubation and that these data were confirmed by the transmission electron microscopy of autophagosome/autophagolysosome formation. RL2 stimulates reactive oxygen species (ROS) production, autophagosomes accumulation, upregulation of ATG5 with processing of LC3I to LC3II, and downregulation of p62/sequestosome 1 (p62).

We have shown that autophagy modulators, CQ, Ku, and Rap, synergistically increased cytotoxicity of RL2, and RL2 with CQ induced autophagic cell death. In addition, CQ, Ku, and Rap in combination with RL2 decreased activity of lysosomal protease Cathepsin D. More importantly, combining RL2 with CQ, we improved antitumor effect in mice. Detected synergistic cytotoxic effects of both types of autophagy regulators, inhibitors, and inducers with RL2 against cancer cells allow us to believe that these combinations can be a basis for the new anticancer approach. Finally, we suppose that CQ and Rap promoting of short-term RL2-induced autophagy interlinks with final autophagic cell death.
We have fulfilled in silico research of number, structure, distribution and location of direct and inverted repeated sequences in eight complete genomes of unicellular cyanobacteria.

Analysis of whole genome repeats has shown utility of this approach for purposes of molecular phylogeny and ecological genomics. Comparative analysis of nonrandom repeats patterns has allowed:

1) to confirm the close genetic relationship of two Prochlorococcus marinus strains (MED4 and SS120) that have reduced genomes and inhabit the econiches with different light intensities; 2) to suggest the close phylogenetic relationship of genomes Prochlorococcus marinus MIT9313 and Synechococcus WH8102 that significantly differ by sets of lightharvesting photosystem; 3) to reveal specific differences in genome organization between marine and freshwater cyanobacteria.
We study numerically the thermoelectricity of the classical Wigner crystal placed in a periodic potential and being in contact with a thermal bath modeled by the Langevin dynamics.

At low temperatures the system has sliding and pinned phases with the Aubry transition between them. We show that in the Aubry pinned phase the dimensionless Seebeck coefficient can reach very high values of several hundreds. At the same time the charge and thermal conductivity of the crystal drop significantly inside this phase.

Still we find that the largest values of ZT factor are reached in the Aubry phase and for the studied parameter range we obtain . We argue that this system can provide an optimal regime for reaching high ZT factors and realistic modeling of thermoelecriticy. Possible experimental realizations of this model are discussed.
Hyperpolarized (HP) propane is a promising contrast agent for magnetic resonance imaging (MRI) of lungs and for studying porous media. The parahydrogen-induced polarization (PHIP) technique is a convenient approach to produce pure propane gas with enhanced proton polarization, when hydrogenation of propylene with parahydrogen is performed over heterogeneous catalysts. Here, we present a new approach of multidimensional mapping of the efficiency of pairwise parahydrogen addition using PHIP-echo pulse sequence. We use this approach to study the performance of three model heterogeneous Rh/TiO2 catalysts in the production of HP propane gas. The three catalysts with 1.0, 13.7, and 23.2 wt % of supported rhodium nanoparticles have been characterized by X-ray photoelectron spectroscopy (XPS) and high resolution transition electron microscopy (HRTEM). By varying the fractions of parahydrogen and propylene in the reactant mixture as well as the gas mixture pressure, 2D maps of PHIP-echo NMR signal and 2D maps of HP propane NMR signal enhancement were obtained. These maps clearly indicate that lower metal coverage results in more efficient pairwise hydrogen addition, producing greater levels of proton polarization of propane gas. The presented method can be extended to multidimensional characterization of the influence of other key parameters of PHIP reaction process including temperature or addition of an inert carrier gas. A 2D T1 relaxation map of propane at 9.4 T is also reported as a function of propane fraction (in the mixture with hydrogen) and gas mixture pressure.
We have obtained analytical solutions for Para-Hydrogen Induced Polarization (PHIP) for several types of coupled spin systems, namely, for AB-, ABX-, AA´A ´´ - and A 2 B-systems. Scalar spin-spin interactions were considered the factor, that determines the PHIP spectral pattern; it is the variation of the spin coupling regime (from strong coupling at low field to weak coupling at high field), which is responsible for the PHIP magnetic field dependence. The field dependence of polarization was considered in detail, general peculiarities of PHIP were found, PHIP patterns were calculated for the systems mentioned. Special attention was paid to the effects of field switching on PHIP.
MicroRNAs proceeds through the different canonical and non-canonical pathways; the most frequent of the non-canonical ones is the splicing-dependent biogenesis of mirtrons. We compare the mirtrons and non-mirtrons of human and mouse to explore how their maturation appears in the precursor structure around the miRNA. We found the coherence of the overhang lengths what indicates the dependence between the cleavage sites. To explain this dependence we suggest the 2-lever model of the Dicer structure that couples the imprecisions in Drosha and Dicer. Considering the secondary structure of all animal pre-miRNAs we confirmed that single-stranded nucleotides tend to be located near the miRNA boundaries and in its center and are characterized by a higher mutation rate. The 5′ end of the canonical 5′ miRNA approaches the nearest single-stranded nucleotides what suggests the extension of the loop-counting rule from the Dicer to the Drosha cleavage site. A typical structure of the annotated mirtron pre-miRNAs differs from the canonical pre-miRNA structure and possesses the 1- and 2 nt hanging ends at the hairpin base. Together with the excessive variability of the mirtron Dicer cleavage site (that could be partially explained by guanine at its ends inherited from splicing) this is one more evidence for the 2-lever model. In contrast with the canonical miRNAs the mirtrons have higher snp densities and their pre-miRNAs are inversely associated with diseases. Therefore we supported the view that mirtrons are under positive selection while canonical miRNAs are under negative one and we suggested that mirtrons are an intrinsic source of silencing variability which produces the disease-promoting variants. Finally, we considered the interference of the pre-miRNA structure and the U2snRNA:pre-mRNA basepairing. We analyzed the location of the branchpoints and found that mirtron structure tends to expose the branchpoint site what suggests that the mirtrons can readily evolve from occasional hairpins in the immediate neighbourhood of the 3′ splice site. The miRNA biogenesis manifests itself in the footprints of the secondary structure. Close inspection of these structural properties can help to uncover new pathways of miRNA biogenesis and to refine the known miRNA data, in particular, new non-canonical miRNAs may be predicted or the known miRNAs can be re-classified.
Flow regimes of immiscible ionic liquid - water flow in T-shaped microchannels with 160 um hydraulic diameter and 1:2 and 1:4 aspect ratios are experimentally studied in the present work. Plug length and velocity were measured using high-speed visualization of the flow.

Flow pattern maps were drawn for two channels. Parallel flow was shown to prevail for 1:4 aspect ratio channel in comparison to 1:2.
We present a study on the evolution of both transverse and longitudinal energy distributions due to oxygen–induced quantum efficiency degradation in the electrons emitted from a reflection–mode p-GaAs(Cs,O)-photocathode over an effective electron affinity range of χ * ∼ −0.1 eV to χ * ∼ +0.3 eV under illumination wavelengths λ = 808, 635 and 532 nm. For λ = 635 and 532 nm, we found that the mean transverse energy of electrons emitted as the photocathode effective electron affinity increased has a non–monotonic character. Our proposed fitting model links the measured response to changes in the relative number of thermalised and non–thermalised electrons in the total emitted photocurrent.
Information visualization is a process of transformation of large and complex abstract forms of information into the visual forms, strengthening cognitive abilities of users and allowing them to take the most optimal decisions.

A graph is an abstract structure that is widely used to model complex information for its visualization.

In the paper, we consider a system aimed at supporting of visualization of big amounts of complex information on the base of attributed hierarchical graphs.
The article presents the results of an analysis of collections and works written by the Old Believers in the 17th – 18th centuries, in order to find out how they used fragments from the works of their ideological opponents. Attention is drawn to the fact that the first generation of defenders of the Old Believers has used quotations from works written in defense of the church reform in order to refute the argument justifying the changes introduced into the rite and the liturgical practice of the Russian Orthodox Church. This method, inherited from Ancient Russia became traditional for the Old Believers. Gradually they began to use parts from the writings of official church representatives to substantiate their point of view on controversial issues. Analysis of the collection of preparatory materials for the «Dyakon Answers» gave an opportunity to understand how the theoretical basis for such an attitude to fragments from opponents’ materials appeared. An analysis of the relevant texts of the collection made it possible to show that a fragment was usually taken out of context and interpreted according to the goals of the Old Believers. As a result, quotes from the works of opponents turned into arguments supporting the Old Believers' point of view in discussions. The texts were quoted «word-for-word», without context but with the appropriate interpretation. «Evidence» was selected in accordance with special principles, for example, «according to the ancient Saints» or «enemies are correct in saying». It was stressed that the enemies were doing it «involuntarily» and «unwillingly». All this allowed the Old Believers to use fragments from anti-Old Believer works in authors writings and collections as authoritative arguments to confirm their interpretation of the church reform initiated by Patriarch Nikon.
Facile and high-yielding procedures for synthesis of monocarboxylic acid derivatives of triarylmethyl radicals (TAMs) were developed.

Reaction of methyl thioglycolate with tris(2,3,5,6-tetrathiaaryl)methyl cation smoothly afforded the monosubstituted TAM derivative, which was hydrolyzed to a monocarboxylic acid, with the TAM moiety attached to thioglycolic acid via the sulfur atom. Alternatively, the diamagnetic tricarboxylic acid precursor of Finland trityl was transformed to a trimethyl ester and partially hydrolyzed under controlled conditions. The diester product was isolated and the remaining fractions were converted back to the trimethyl ester for production of more diester.

The first representatives of TAM biradicals with different TAM cores and interspin distances were obtained by reaction of these new TAM monocaboxylic acids with N,N'-dimethylethylenediamine.