Hengzongshu/ArticleAgent huggingface dataset:
How chromosomes are folded, spatially organized and regulated in three dimensions inside the cell nucleus are among the longest standing questions in cell biology. Genome-wide chromosome conformation capture (Hi-C) technique allowed identifying and characterizing spatial chromatin compartments in several mammalian species.

Here, we present the first genome-wide analysis of chromatin interactions in chicken embryonic fibroblasts (CEF) and adult erythrocytes. We showed that genome of CEF is partitioned into topologically associated domains (TADs), distributed in accordance with gene density, transcriptional activity and CTCF-binding sites.

In contrast to mammals, where all examined somatic cell types display relatively similar spatial organization of genome, chicken erythrocytes strongly differ from fibroblasts, showing pronounced A- and B- compartments, absence of typical TADs and formation of long-range chromatin interactions previously observed on mitotic chromosomes. Comparing mammalian and chicken genome architectures, we provide evidence highlighting evolutionary role of chicken TADs and their significance in genome activity and regulation.
Let [Formula: see text] be a short exact sequence of Lie algebras over a field [Formula: see text], where [Formula: see text] is abelian. We show that the obstruction for a pair of automorphisms in [Formula: see text] to be induced by an automorphism in [Formula: see text] lies in the Lie algebra cohomology [Formula: see text]. As a consequence, we obtain a four term exact sequence relating automorphisms, derivations and cohomology of Lie algebras. We also obtain a more explicit necessary and sufficient condition for a pair of automorphisms in [Formula: see text] to be induced by an automorphism in [Formula: see text], where [Formula: see text] is a free nilpotent Lie algebra of rank [Formula: see text] and step [Formula: see text].
Diseases of cereals caused by pathogenic fungi can significantly reduce crop yields. Many cultures are exposed to them. The disease is difficult to control on a large scale; thus, one of the relevant approaches is the crop field monitoring, which helps to identify the disease at an early stage and take measures to prevent its spread. One of the effective control methods is disease identification based on the analysis of digital images, with the possibility of obtaining them in field conditions, using mobile devices. In this work, we propose a method for the recognition of five fungal diseases of wheat shoots (leaf rust, stem rust, yellow rust, powdery mildew, and septoria), both separately and in case of multiple diseases, with the possibility of identifying the stage of plant development. A set of 2414 images of wheat fungi diseases (WFD2020) was generated, for which expert labeling was performed by the type of disease. More than 80% of the images in the dataset correspond to single disease labels (including seedlings), more than 12% are represented by healthy plants, and 6% of the images labeled are represented by multiple diseases. In the process of creating this set, a method was applied to reduce the degeneracy of the training data based on the image hashing algorithm. The disease-recognition algorithm is based on the convolutional neural network with the EfficientNet architecture. The best accuracy (0.942) was shown by a network with a training strategy based on augmentation and transfer of image styles. The recognition method was implemented as a bot on the Telegram platform, which allows users to assess plants by lesions in the field conditions.
The method is based on the original scanning flow cytometer that measures angle‐resolved light‐scattering patterns (LSPs) of individual particles.

We modeled the shape of E. coli cells as a cylinder capped with hemispheres of the same radius, and simulated light scattering by the models using the discrete dipole approximation. We computed a database of the LSPs of individual bacteria in a wide range of model parameters and used it to solve the inverse light‐scattering problem by the nearest‐neighbor interpolation.

The developed method was tested on two strains of E. coli. The resulting precision of bacteria length and diameter measurements varied from 50 nm to 250 nm and from 5 nm to 25 nm, respectively. The measured distributions of samples over length and diameter were in good agreement with measurements performed by optical microscopy and literature data. The described approach can be applied for rapid morphological characterization of any rod‐shaped bacteria.
Chromosome 1 with one or two long insertions has been previously found in natural mouse populations. The inheritance of chromosome 1 with two insertions from the Yakutsk population is analysed in this paper. It was demonstrated that heterozygous females transmit this chromosome to 80-85% of offspring. The observations made at M II, in conjunction with the recombination data, allowed us to conclude that preferential passage of the chromosome 1 with insertions to the oocyte and egg, rather than to the first and second polar bodies at meiosis, is the causative factor of the distorted segregation. A meiotic drive of such potency has not been previously reported for female mammals. The possible mechanism of the drive is discussed.
The purpose of the study is to gain an insight into the current language situation among speakers of the German dialects in two largest regions of Siberia - Novosibirsk Oblast and Tomsk Oblast.

The work is novel in that it introduces data from new field researches into scientific use. In addition to that, the language situation among speakers of the German dialects is for the first time assessed basing on the idioms forming it (they are represented by dialects of the Low and High German varieties) and their demographic power.

The research findings amount to describing the language situation on the basis of a theoretical analysis of the facts obtained empirically while collecting material in the dialects in the field.
An experimental study, implicated in the revealing of the conditions for the origin for Fe3+-bearing magnesiowüstite in the lithospheric mantle, was performed using Mössbauer spectroscopy of pre-synthesized samples.

Experiments were carried out using a multi-anvil high-pressure split-sphere apparatus at 6.3–7.5 GPa, in the range of 1100–1650 °C in carbonate-metal, carbonate–oxide-metal, carbonate-oxide, carbide-oxide and carbonate–metal- sulphur systems. In three experimental series, oxygen fugacity gradient in the samples was created, which enabled the study of the processes of magnesiowüstite formation under oxidizing and reducing conditions (ΔlogfO2 (FMQ) values from −1 to −5). According to the Mössbauer spectroscopy, the composition of synthesized magnesiowüstite varied within a range of Fe3+/ΣFe values from 0 to 0.3, with IV and VI coordination of Fe3+ depending on P, T, fO2, x-parameters.

It was established that Fe3+-bearing magnesiowüstite can form both in assemblage with oxidized phases, such as carbonate or with reduced ones—metal, carbides, sulphides, graphite and diamond. It was established that Fe3+-bearing magnesiowüstite formation processes under upper mantle P,T-conditions include redox reactions, with magnesiowüstite being (1) reductant or (2) product of interaction, (3) crystallization processes of magnesiowüstite from an oxidized melt, where magnesiowüstite acts as a sink for ferric iron and (4) iron disproportionation.
Using $535\ifmmode\times\else\texttimes\fi{}{10}^{6}$ $B$-meson pairs collected by the Belle detector at the KEKB ${e}^{+}{e}^{\ensuremath{-}}$ collider, we measure branching fractions of $(7.16\ifmmode\pm\else\textpm\fi{}0.10(\mathrm{stat})\ifmmode\pm\else\textpm\fi{}0.60(\mathrm{syst})\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}4}$ for ${B}^{+}\ensuremath{\rightarrow}J/\ensuremath{\psi}{K}^{+}{\ensuremath{\pi}}^{+}{\ensuremath{\pi}}^{\ensuremath{-}}$ and $(4.31\ifmmode\pm\else\textpm\fi{}0.20(\mathrm{stat})\ifmmode\pm\else\textpm\fi{}0.50(\mathrm{syst}))\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}4}$ for ${B}^{+}\ensuremath{\rightarrow}{\ensuremath{\psi}}^{\ensuremath{'}}{K}^{+}{\ensuremath{\pi}}^{+}{\ensuremath{\pi}}^{\ensuremath{-}}$. We perform amplitude analyses to determine the resonant structure of the ${K}^{+}{\ensuremath{\pi}}^{+}{\ensuremath{\pi}}^{\ensuremath{-}}$ final state in ${B}^{+}\ensuremath{\rightarrow}J/\ensuremath{\psi}{K}^{+}{\ensuremath{\pi}}^{+}{\ensuremath{\pi}}^{\ensuremath{-}}$ and ${B}^{+}\ensuremath{\rightarrow}{\ensuremath{\psi}}^{\ensuremath{'}}{K}^{+}{\ensuremath{\pi}}^{+}{\ensuremath{\pi}}^{\ensuremath{-}}$ and find that the ${K}_{1}(1270)$ is a prominent component of both decay modes. There is significant interference among the different intermediate states, which leads, in particular, to a striking distortion of the $\ensuremath{\rho}$ line shape due to the $\ensuremath{\omega}$. Based on the results of the fit to the ${B}^{+}\ensuremath{\rightarrow}J/\ensuremath{\psi}{K}^{+}{\ensuremath{\pi}}^{+}{\ensuremath{\pi}}^{\ensuremath{-}}$ data, the relative decay fractions of the ${K}_{1}(1270)$ to $K\ensuremath{\rho}$, $K\ensuremath{\omega}$, and ${K}^{*}(892)\ensuremath{\pi}$ are consistent with previous measurements, but the decay fraction to ${K}_{0}^{*}(1430)$ is significantly smaller. Finally, by floating the mass and width of the ${K}_{1}(1270)$ in an additional fit of the ${B}^{+}\ensuremath{\rightarrow}J/\ensuremath{\psi}{K}^{+}{\ensuremath{\pi}}^{+}{\ensuremath{\pi}}^{\ensuremath{-}}$ data, we measure a mass of $(1248.1\ifmmode\pm\else\textpm\fi{}3.3(\mathrm{stat})\ifmmode\pm\else\textpm\fi{}1.4(\mathrm{syst}))\text{ }\text{ }\mathrm{MeV}/{c}^{2}$ and a width of $(119.5\ifmmode\pm\else\textpm\fi{}5.2(\mathrm{stat})\ifmmode\pm\else\textpm\fi{}6.7(\mathrm{syst}))\text{ }\text{ }\mathrm{MeV}/{c}^{2}$ for the ${K}_{1}(1270)$.
We report the first observation of the double strange baryon Ξ(1620)^{0} in its decay to Ξ^{-}π^{+} via Ξ_{c}^{+}→Ξ^{-}π^{+}π^{+} decays based on a 980 fb^{-1} data sample collected with the Belle detector at the KEKB asymmetric-energy e^{+}e^{-} collider. The mass and width are measured to be 1610.4±6.0(stat)_{-4.2}^{+6.1} (syst) MeV/c^{2} and 59.9±4.8(stat)_{-7.1}^{+2.8}(syst) MeV, respectively. We obtain 4.0σ evidence of the Ξ(1690)^{0} with the same data sample. These results shed light on the structure of hyperon resonances with strangeness S=-2.
Medical genomics relies on next-gen sequencing methods to decipher underlying molecular mechanisms of gene expression. This special issue collects materials originally presented at the "Centenary of Human Population Genetics" Conference-2019, in Moscow.

Here we present some recent developments in computational methods tested on actual medical genetics problems dissected through genomics, transcriptomics and proteomics data analysis, gene networks, protein-protein interactions and biomedical literature mining. We have selected materials based on systems biology approaches, database mining. These methods and algorithms were discussed at the Digital Medical Forum-2019, organized by I.M. Sechenov First Moscow State Medical University presenting bioinformatics approaches for the drug targets discovery in cancer, its computational support, and digitalization of medical research, as well as at "Systems Biology and Bioinformatics"-2019 (SBB-2019) Young Scientists School in Novosibirsk, Russia.

Selected recent advancements discussed at these events in the medical genomics and genetics areas are based on novel bioinformatics tools.
Hydrogenated amorphous silicon (a‐Si:H) films were studied using infrared and Raman spectroscopy. We have experimentally found that ratios of Raman scattering cross‐sections for Si–H to Si–Si bonds and for Si–H 2 to Si–Si bonds are equal to 0.65 ± 0.07 and 0.25 ± 0.03, respectively. It allows to measure the concentration of hydrogen in a‐Si:H films. The developed approach can be applied for in situ control of hydrogen in a‐Si:H films and also suitable for thin a‐Si:H films on substrates that are opaque in infrared spectral region. Copyright © 2013 John Wiley & Sons, Ltd.
Золоторудные объекты в скарнах широко распространены в геологических структурах Восточной Тувы, но их промышленная оценка сопряжена со значительными трудностями из-за слабой изученности их минералого-геохимических особенностей. Актуальность исследования обусловлена необходимостью расшифровки генезиса и условий образования золоторудных объектов, локализованных в скарнах.

Методы: полевые исследования, детальные минералогические исследования с изучением рудной минерализации в полированных шлифах (аншлифах) с помощью сканирующего электронного микроскопа Tescan Vega 3 sbu с ЭДС Oxford Instruments X-act. Условия формирования минеральных ассоциаций определялись термобарогеохимическими методами.

Результаты. Установлено, что золоторудная минерализация на месторождении Барсучий является постскарновой и имеет гидротермальный генезис, образуя прожилково-вкрапленное и прожилковое оруденение штокверкового типа в диоритах, контактовых (роговики, скарны) и гидротермально-метасоматических породах. Околорудные процессы на месторождении выражены в березитизации и лиственитизации кварцевых диоритов, скарнов и карбонатных пород. Отложение самородного золота происходило в две стадии. По составу продуктивных минеральных ассоциаций Барсучий отвечает золото-пирротин-пирит-халькопиритовому типу с калаверитом AuTe2, петцитом Ag3AuTe2, гесситом Ag2Te и минералами ряда теллуровисмутит-теллурантимон. Рудоотложение золота на месторождении происходило из водных растворов с хлоридами Na и K, содержащих CO2 и CH4, с солёностью 1,7−10,5 мас. % NaCl-экв. при изменении окислительно-восстановительного потенциала среды при вариациях f S2, f Se2, f Te2 и снижении температуры рудоносного флюида (первая продуктивная стадия – 360–280 °С, вторая – 320–240 °С). По минералого-геохимическим особенностям месторождение Барсучий относится к малосульфидной золото-сульфидно-кварцевой формации и близко к месторождениям золото-висмутового геохимического типа.
Traditionally, studies of the neurobiology of learning and memory focus on the circuitry that interfaces between sensory inputs and behavioral outputs, such as the amygdala and cerebellum. However, evidence is accumulating that some forms of learning can in fact drive stimulus-specific changes very early in sensory systems, including not only primary sensory cortices but also precortical structures and even the peripheral sensory organs themselves.

In this study, we investigated the effect of olfactory associative training on the functional activity of olfactory epithelium neurons in response to an indifferent stimulus (orange oil). To interpret the results obtained, we compared the distribution of MRI contrast across the zones of OE in response to a conditioned odor in trained animals and in control animals that were given orange oil at three concentrations: original (used for conditioning), 4-fold higher and 4-fold lower.

It was found that such a peripheral structure of the olfactory system of adult mice as the olfactory epithelium (OE) demonstrates experience-dependent plasticity. Associative learning led to changes in the patterns of OE cell activation in response to orange oil. Since the OE activation patterns obtained coincided in the group of trained animals and controls, which were stimulated with orange oil at the 4-fold higher concentration, it can be concluded that associative conditioning increased the sensitivity of the OE to the conditioned stimulus. The observed increase in OE response to orange oil may be the result of neurogenesis or the consequence of an increase in individual sensitivity of each OE neuron. Based on data of MRI contrast accumulation in mouse OE, the sensory plasticity way in learning-induced increase in sensitivity of OE to conditioned stimulus is more possible. Thus, the sensory plasticity of the OE plays a significant role in the formation of the neuronal response to the provision of an initially indifferent odor and is part of the adaptive responses to the environmental changing.
The article poses a problem of engineering education and training of today, which are facing difficulties while developing an efficient competency-based approach realization.

The authors concentrate on an urgent task of developing the integration competence of future engineers which is treated as a metadisciplinary competence providing students with ability and readiness to synthesize subject-oriented professional and social competences into a holistic system. The structure of integration competence is analyzed and the following components are determined: a value and motivation component; a practical activity component; a cognitive component; a self-analysis and self-assessment component. Among distinguishing features of the integration competence the authors define its instrumental character, metadisciplinary and universal properties as well as its nonalgorithmic character. It is shown that professionally oriented training is a core factor of integration competence development. Depending on elements being integrated, the main forms of integration of competences are determined.

The model of competence integration presented in the article can serve as the basis for developing methods and conditions for its systematic elaboration in university training. The results of this study can be useful for educators of different administrative levels, teaching-and-training schools which realize a competency-based approach in their teaching.
Six new metal-organic frameworks based on 2,5-thiophendicarboxylate (tdc2–) and zinc(II) ions were prepared in different reaction conditions, and their crystal structures were determined by XRD analysis. The compound [Zn(tdc)(dabco)(H2O)]∙DMF (1) is based on mononuclear Zn(II) ions connected by tdc2– and dabco linkers into square-grid layered nets. The compound [Zn3(tdc)3(dabco)2] (2) is a rare example of monocoordinated dabco ligands in the metal-organic framework chemistry. Its crystal structure contains trinuclear linear carboxylate building units, connected into a distorted primitive cubic net. Similar trinuclear units were also found in [Zn5(tdc)4(Htdc)2(dabco)2]∙4DMF∙14H2O (3), although as a part of more complicated pentanuclear motives. The compound [Na2Zn(tdc)2(DMF)2] (4), quantitatively isolated by the addition of NaOH to the mixture of Zn(NO3)2 and H2tdc, is based on 1D chain motives, interconnected by tdc2– linkers into a three-dimensional framework. The compounds [Zn3(tdc)3(DMF)2]∙0.8DMF∙1.1H2O (5) and [Zn3(tdc)3(DMF)3]∙0.8DMF∙1.3H2O (6) were prepared in very similar reaction conditions, but with different times of heating, indirectly indicating higher thermodynamic stability of the three-dimensional metal-organic framework 6, compared to the two-dimensional metal-organic framework 5. The crystal structures of both 5 and 6 are based on the same trinuclear linear units as in 2. Luminescence properties of the compounds 4–6 were studied and compared with those for Na2tdc salt. In particular, the luminescence spectra of 4 practically coincide with those for the reference Na2tdc, while 5 and 6 exhibit coherent shifts of peaks to higher energies. Such hypsochromic shifts are likely associated with a different effective charge on the tdc2– anions in Na2tdc and sodium-containing 4, compared to zinc-based 5 and 6.
This work describes the nearly complete genome sequence of Newcastle disease virus (NDV) strain NDV/Novosibirsk/garganey/27/2014, which was isolated from a wild garganey in western Siberia, Russia. The NDV strain was classified as belonging to class II of genotype I and was identified as having recent common ancestry with isolates from wild and domestic birds in China and South Korea.
By applying an old result of Y. Berkovich

we provide a polynomial-time algorithm for computing the minimal possible index of a proper subgroup of a finite permutation group [Formula: see text]. Moreover, we find that subgroup explicitly and within the same time if [Formula: see text] is given by a Cayley table

As a corollary, we get an algorithm for testing whether or not a finite permutation group acts on a tree non-trivially
Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide with limited therapeutic options. Since HCC has been shown to be immunogenic, immunotherapy is considered a promising therapeutic approach. Small interfering RNAs (siRNAs), depending on their structure and sequence, can trigger the innate immune system, which can potentially enhance the adaptive anticancer immune response in the tumor-bearing subjects. Immunostimulatory properties of nucleic acids can be applied to develop adjuvants for HCC treatment. The transplantable HCC G-29 tumor in male CBA/LacSto (CBA) mice was used to study the effects of immunostimulatory RNA on tumor growth. Tumor size, metastases area in different organs of mice and mouse survival rate were analyzed. Furthermore the mouse serum IFN-α levels were measured using ELISA. In the present study, we found that a 19-bp RNA duplex (ImmunoStimulattory RNA or isRNA) with 3-nt overhangs at the 3′-ends of specific sequence displays immunostimulatory, antitumor, and antimetastatic activities in mice bearing HCC G-29. Our results demonstrate that isRNA strongly increases the level of interferon-α (IFN-α) by up to 25-fold relative to the level in mice injected with Lipofectamine alone (Mock), and to a lesser extent increases the level of proinflammatory cytokine interleukin-6 (IL-6) (by up to 5.5-fold relative to the Mock level), in mice blood serum. We showed that isRNA reliably (P < 0.05) inhibits primary tumor growth in mice compared to the mock group. Furthermore, injections of isRNA significantly enhanced necrotic processes in the center of the primary tumor, and decreased by twofold the width of the undifferentiated peripheral zone and the number of mitotic cells in this zone. The results showed that isRNA efficiently reduces the area of metastases in the liver, kidneys, and heart of CBA/LacSto mice with HCC. The obtained results clearly demonstrate immunostimulatory and antimetastatic properties of the isRNAs in mice with HCC. Consequently, this short double-stranded RNA can be considered as a potential adjuvant for the therapy of HCC.
Precision measurements of the heat capacity of thulium 1-2-3 cuprate with oxygen concentrations x=6.92 and x=6.7 are made in the temperature range 6–300 K.

After the lattice components of the heat capacity of the samples are subtracted off, a comparison of the results makes it possible to determine the contribution to the heat capacity due to the formation of the pseudogap phase for the sample with x=6.7.

The temperature dependence of this contribution has an anomaly near the boundary of the transition from the pseudogap phase to the normal metallic phase. The experimental results correlate with the theoretical ideas about the rearrangement of the electronic structure upon the transition of the system to the pseudogap phase region.
Axial and radial distributions of the rotational temperature and density of N2 molecules in supersonic nitrogen jets formed with conic nozzles (critical diameters dcr of 0.17 and 0.21 mm) were studied using the electron beam fluorescence technique at stagnation pressures P0 of 0.1-0.6 MPa. A rotational temperature Tr, equaling a gas temperature Tg owing to fast RT relaxation, was obtained using the rotational line relative intensity distribution in (0-1) vibrational band of the N2 first negative system. Gas density profiles in the jets were obtained using the integral intensity of the band. It is found, Tr at the nozzle outlet is of the order of a few tens of Kelvin and at further expansion Tr drops up to 15-20K at distance of (100-200) dcr. The gas temperature and density distributions in the studied supersonic nitrogen jets are not similar to the isentropic distributions. It is shown that the lower is the stagnation pressure the faster the gas density and temperature decrease with distance from the nozzle. Increase in P0 leads to elevating Tg in the jets. A reason for this effect may be cluster formation in the jets. Estimations of cluster mean sizes in the jets using Hagena's parameter show presence of large clusters (M≥200) at P0 = 0.4-0.6 MPa.