Hengzongshu/ArticleAgent huggingface dataset:
Neuronal tracing is a modern technology that is based on the expression of fluorescent proteins under the control of cell type–specific promoters. However, random genomic integration of the reporter construct often leads to incorrect spatial and temporal expression of the marker protein. Targeted integration (or knock‐in) of the reporter coding sequence is supposed to provide better expression control by exploiting endogenous regulatory elements. Here we describe the generation of two fluorescent reporter systems: enhanced green fluorescent protein (EGFP) under pan‐neural marker class III β‐tubulin ( Tubb3 ) promoter and mEos2 under serotonergic neuron‐specific tryptophan hydroxylase 2 ( Tph2 ) promoter. Differentiation of Tubb3‐EGFP embryonic stem (ES) cells into neurons revealed that though Tubb3‐positive cells express EGFP, its expression level is not sufficient for the neuronal tracing by routine fluorescent microscopy. Similarly, the expression levels of mEos2‐TPH2 in differentiated ES cells was very low and could be detected only on messenger RNA level using polymerase chain reaction‐based methods. Our data shows that the use of endogenous regulatory elements to control transgene expression is not always beneficial compared with the random genomic integration.
A search for the flavor-changing neutral-current decay B^{+}→K^{+}νν[over ¯] is performed at the Belle II experiment at the SuperKEKB asymmetric energy electron-positron collider. The data sample corresponds to an integrated luminosity of 63 fb^{-1} collected at the ϒ(4S) resonance and a sample of 9 fb^{-1} collected at an energy 60 MeV below the resonance.

Because the measurable decay signature involves only a single charged kaon, a novel measurement approach is used that exploits not only the properties of the B^{+}→K^{+}νν[over ¯] decay, but also the inclusive properties of the other B meson in the ϒ(4S)→BB[over ¯] event, to suppress the background from other B meson decays and light-quark pair production. This inclusive tagging approach offers a higher signal efficiency compared to previous searches.

No significant signal is observed. An upper limit on the branching fraction of B^{+}→K^{+}νν[over ¯] of 4.1×10^{-5} is set at the 90% confidence level.
Despite the economic importance of creating cold resilient cattle breeds, our knowledge of the genetic basis of adaptation to cold environments in cattle is still scarce compared to information on other economically important traits. Herein, using whole-genome resequencing of animals showing contrasting phenotypes on temperature maintenance under acute cold stress combined with the existing SNP (single nucleotide polymorphism) functional annotations, we report chromosomal regions and candidate SNPs controlling body temperature in the Siberian cattle populations. The SNP ranking procedure based on regional FST calculations, functional annotations, and the allele frequency difference between cold-tolerant and cold-sensitive groups of animals pointed to multiple candidate genes. Among these, GRIA4, COX17, MAATS1, UPK1B, IFNGR1, DDX23, PPT1, THBS1, CCL5, ATF1, PLA1A, PRKAG1, and NR1I2 were previously related to thermal adaptations in cattle. Other genes, for example KMT2D and SNRPA1, are known to be related to thermogenesis in mice and cold adaptation in common carp, respectively. This work could be useful for cattle breeding strategies in countries with harsh climates, including the Russian Federation.
Thousands of long non-coding RNA (lncRNA) genes are annotated in the human genome. Recent studies showed the key role of lncRNAs in a variety of fundamental cellular processes. Dysregulation of lncRNAs can drive tumorigenesis and they are now considered to be a promising therapeutic target in cancer. However, how lncRNAs contribute to the development of hereditary diseases in human is still mostly unknown.

This review is focused on hereditary diseases in the pathogenesis of which long non-coding RNAs play an important role. Fundamental research in the field of molecular genetics of lncRNA is necessary for a more complete understanding of their significance.

Future research will help translate this knowledge into clinical practice which will not only lead to an increase in the diagnostic rate but also in the future can help with the development of etiotropic treatments for hereditary diseases.
We analyze the applicability of the smooth particle hydrodynamics (SPH) to the solution of boundary value problems involving large deformation of solids. The main focus is set on such issues as the reduction of artificial edge effects by implementing corrected kernels and their gradients, accurate and efficient computation of the deformation gradient tensor, evaluation of the internal forces from the given stress field. For demonstration purposes, a hyperelastic body of neo-Hookean type and a visco-elastic body of Maxwell type are considered; the formulation of the Maxwell material is based on the approach of Simo and Miehe (1992). For the implementation of constitutive relations efficient and robust numerical schemes are used. A solution for a series of test problems is presented. The performance of the implemented algorithms is assessed by checking the preservation of the total energy of the system. As a result, a functional combination of SPH-techniques is identified, which is suitable for problems involving large strains, rotations and displacements coupled to inelastic material behaviour. The accuracy of the SPH-computations is assessed using nonlinear FEM as a benchmark.
Full Bayesian inference for detecting copy number variants (CNV) from whole-genome sequencing (WGS) data is still largely infeasible due to computational demands. A recently introduced approach to perform Forward-Backward Gibbs sampling using dynamic Haar wavelet compression has alleviated issues of convergence and, to some extent, speed. Yet, the problem remains challenging in practice.In this paper, we propose an improved algorithmic framework for this approach. We provide new space-efficient data structures to query sufficient statistics in logarithmic time, based on a linear-time, in-place transform of the data, which also improves on the compression ratio. We also propose a new approach to efficiently store and update marginal state counts obtained from the Gibbs sampler.Using this approach, we discover several CNV candidates in two rat populations divergently selected for tame and aggressive behavior, consistent with earlier results concerning the domestication syndrome as well as experimental observations. Computationally, we observe a 29.5-fold decrease in memory, an average 5.8-fold speedup, as well as a 191-fold decrease in minor page faults. We also observe that metrics varied greatly in the old implementation, but not the new one. We conjecture that this is due to the better compression scheme. The fully Bayesian segmentation of the entire WGS data set required 3.5 min and 1.24 GB of memory, and can hence be performed on a commodity laptop.
Screening of the Coulumb interaction accounting for the Friedel oscillations in the structures with multicomponent low-dimensional electron plasma is considered.

Calculations are made for nanotubes, double quantum wells (DQW) and superlattices.

The binding energy of a donor in DQW is found as a function of the subbands occupation numbers.
Биоинформационным анализом обнаружено в общей сложности 55 генов

На хромосомах 2A и 2D мягкой пшеницы установлены позиции 'hot spot' локусов, важных для регуляции ответов на водный дефицит
This study had evaluated three commercially available bisulfite modification kits with regard to the procedural DNA loss and the efficacy of cytosine conversion to uracil.

The efficacy of DNA conversion was estimated by pyrosequencing of eight CpG sites of unmethylated and fully enzymatically methylated templates of RARβ gene promoter region and cirDNAs of healthy donors and prostate cancer patients. The procedural DNA loss was calculated by methyl-independent qPCR for ubiquitously distributed L1RE1 retrotransposable elements.

Our data demonstrates that all commercial kits displayed similar conversion efficacy of the unmethylated cytosines close to 99% independently of DNA concentration. However, when low DNA concentrations were used, the observed basic level of genomic DNA methylation increased to 11% depending on the position of CpG site. Qiagen and Chemicon kits recovered no more than 20% starting material at a high DNA input (500 ng/probe) and only 2.7–5.8% for low DNA input (10 ng/probe). EZ DNA Methylation-Gold Kit from Zymo Research provided the highest recovery regardless of the initial DNA input with average rates of no less than 86%. These results suggest that the EZ DNA Methylation-Gold Kit is the most appropriate tool for bisulfite modification of cirDNA when assaying DNA in low amounts.
A series of novel deoxycholic acid (DCA) derivatives containing aliphatic diamine and aminoalcohol or morpholine moieties at the C3 position were synthesized by 3,26-epoxide ring-opening reactions.

These compounds were investigated for their cytotoxicity in four human tumor cell lines and murine macrophages and for inhibitory activity against macrophage-mediated NO synthesis in vitro.

Obtained data revealed that: (i) all amine-containing substituents significantly increased the cytotoxicity of the novel compounds (IC502-10 = 1.0-36.0 μM) in comparison with DCA (IC50DCA ≥ 82.9 μM); (ii) aminoalcohol moieties were more preferable than diamine moieties due to the fact they imparted better selectivity for tumor cells of the novel derivatives; (iii) the susceptibility of tested cell lines to derivatives diminished in the following order: HuTu-80 (duodenal carcinoma) ≈ HepG2 (hepatocarcinoma) > KB-3-1 (cervical carcinoma) > RAW264.7 (macrophages) > A549 (lung carcinoma); (iv) compounds 8 and 9, bearing aminoethanol and aminopropanol moieties, respectively, exhibited high cytotoxic selectivity indexes (SIHuTu-80 = 7.9 and 8.3, respectively) and good drug-likeness parameters; (v) the novel compounds do not display anti-NO activity. Mechanistic study revealed that compound 9 induces ROS-dependent cell death by activation of intrinsic caspase-dependent apoptosis and cytodestructive autophagy in HuTu-80 cells and vitamin D receptor can be considered as its primary target.
We study the charge transport mechanism of electron via traps in thermal SiO2 on silicon. Electron transport is limited by phonon-assisted tunnelling between traps. Charge flowing leads to oxygen vacancies generation, and the leakage current increases. Long-time annealing at high temperatures decreased the leakage current to initial values due to oxygen vacancies recombination with interstitial oxygen. Taking into account results of ab initio simulations, we found that the oxygen vacancies act as electron traps in SiO2.
The repair processes regulation including base excision repair (BER) is implemented by a cellular signal PARylation catalysed by PARP1 and PARP2. Despite intensive studies, it is far from clear how BER is regulated by PARPs and how the roles are distributed between the PARPs.

Here, we investigated the effects of PARP1, PARP2 and PARylation on activities of the main BER enzymes (APE1, Polβ and LigIIIα) in combination with XRCC1 in the nucleosomal context. We constructed nucleosomes with midward- or outward-oriented damage.

It was concluded that in most cases, the presence of PARP1 leads to the suppression of the activities of APE1, Polβ, and to a lesser extent LigIIIα. PARylation by PARP1 attenuated this effect to various degrees. PARP2 had an influence predominantly on the last stage of BER: DNA sealing. Nonetheless, PARylation by PARP2 led to Polβ inhibition and to significant stimulation of LigIIIα activities in a NAD + -dependent manner.
The article presents the result of the numerical simulation of the turbulent flow for a rib-step system by the RANS method at the Reynolds number, calculated by the step height and average flow rate velocity, Re = 5000.

The data obtained in these studies showed the influence of divergence ratio on heat transfer in a flat channel with a transverse rib acting as a vortex generator.

It is shown that with an increase in the divergence ratio, the length of the recirculation zone increases, while the position of the heat transfer maximum varies slightly.
Electron states in a quantum dot (QD) located near a 2D system of dipolar excitons are perturbed by fluctuations of the exciton density caused by the electron-exciton interaction. This results in the frequency changes of electron transitions in a QD. The frequency depends on the exciton density, as well as on the exciton gas phase state. In the present work, the shifts of the two lowest QD energy levels are found both in the normal state of the exciton system and for the Bose-Einstein condensation (BEC) regime.
Rectangular microchannels are most common configuration in microfluidics. They can be used in many industries, for example in lab-on-chip devices. Despite standard fluid dynamics, microfluidics has a significant impact of wall boundary conditions on fluid flow. And in microfluidics, we cannot simply set no-slip boundary conditions if our goal is accurate modeling results.

In this paper, a solution is proposed to find a more accurate way to model the fluid flow in a rectangular microchannel by knowing the friction factor without shear stress distribution.

In rectangular microchannels, there is another important moment in modeling that is not present in circular pipes. The velocity profile of the fluid depends on the shear stress at the edges and the velocities at the walls of the microchannel change at different points of the cross-sectional wall of the microchannel. The fluid velocity is lower at the corners of a rectangular microchannel.
ABSTRACT The forkhead boxO transcription factor (FOXO) is a component of the insulin signalling pathway and plays a role in responding to adverse conditions, such as oxidative stress and starvation. In stressful conditions, FOXO moves from the cytosol to the nucleus where it activates gene expression programmes. Here, we show that FOXO in Drosophila melanogaster responds to heat stress as it does to other stressors. The catecholamine signalling pathway is another component of the stress response. In Drosophila, dopamine and octopamine levels rise steeply under heat, nutrition and mechanical stresses, which are followed by a decrease in the activity of synthesis enzymes. We demonstrate that the nearly twofold decline of FOXO expression in foxoBG01018 mutants results in dramatic changes in the metabolism of dopamine and octopamine and the overall response to stress. The absence of FOXO increases tyrosine decarboxylase activity, the first enzyme in octopamine synthesis, and decreases the enzymatic activity of enzymes in dopamine synthesis, alkaline phosphatase and tyrosine hydroxylase, in young Drosophila females. We identified the juvenile hormone as a mediator of FOXO regulation of catecholamine metabolism. Our findings suggest that FOXO is a possible trigger for endocrinological stress reactions.
The experimental data represented in the bibliography are theoretically analyzed to construct an adequate model for dynamics of an open nonequilibrium living system. Relevant published data were used to demonstrate a fractal structure of the space in the vicinity of centrally gravitating bodies with satellites revolving around them along closed trajectories and serving as a kind of testers of the neighboring space.

It is shown that the viable microorganisms are capable of forming the fractal structure, whose dimensionality is certainly non-integral. In addition, we have attempted to provide a generalized description of the properties of living and nonliving matter (in the addition to that described in work [1]).

A local violation of its discontinuity is likely to be a necessary (yet not sufficient!) dynamic characteristic of the spatiotemporal continuum for self-organization of molecules into a living, i.e., self-replicating, system.
Long-term space travel simulation experiments enabled to discover different aspects of human metabolism such as the complexity of NaCl salt balance. Detailed proteomics data were collected during the Mars105 isolation experiment enabling a deeper insight into the molecular processes involved.

We studied the abundance of about two thousand proteins extracted from urine samples of six volunteers collected weekly during a 105-day isolation experiment under controlled dietary conditions including progressive reduction of salt consumption. Machine learning using Self Organizing maps (SOM) in combination with different analysis tools was applied to describe the time trajectories of protein abundance in urine. The method enables a personalized and intuitive view on the physiological state of the volunteers. Regulatory modes associated with distinct biological processes were identified using previous knowledge by applying enrichment and pathway flow analysis.

The abundance of more than one half of the proteins measured clearly changes in the course of the experiment. The trajectory splits roughly into three time ranges, an early (week 1-6), an intermediate (week 7-11) and a late one (week 12-15). Early protein activation modes can be related to immune response and inflammatory processes, activation at intermediate times to developmental and proliferative processes and late activations to stress and responses to chemicals. The protein abundance profiles support previous results about alternative mechanisms of salt storage in an osmotically inactive form. We hypothesize that reduced NaCl consumption of about 6 g/day presumably will reduce or even prevent the activation of inflammatory processes observed in the early time range of isolation. SOM machine learning in combination with analysis methods of class discovery and functional annotation enable the straightforward analysis of complex proteomics data sets generated by means of mass spectrometry.
ACTIVITY is a database on DNA/RNA site sequences with known activity magnitudes, measurement systems, sequence-activity relationships under fixed experimental conditions and procedures to adapt these relationships from one measurement system to another. This database deposits information on DNA/RNA affinities to proteins and cell nuclear extracts, cutting efficiencies, gene transcription activity, mRNA translation efficiencies, mutability and other biological activities of natural sites occurring within promoters, mRNA leaders, and other regulatory regions in pro- and eukaryotic genomes, their mutant forms and synthetic analogues.

Since activity magnitudes are heavily system-dependent, the current version of ACTIVITY is supplemented by three novel sub-databases: (i) SYSTEM, measurement systems; (ii) KNOWLEDGE, sequence-activity relationships under fixed experimental conditions; and (iii) CROSS_TEST, procedures adapting a relationship from one measurement system to another.

These databases are useful in molecular biology, pharmacogenetics, metabolic engineering, drug design and biotechnology. The databases can be queried using SRS and are available through the Web, http://wwwmgs.bionet.nsc.ru/systems/Activity/.
Dark photons and mirror matter are well-motivated dark matter candidates.

It is possible that both of them arose during the compactification and symmetry breaking scenario of the heterotic $E_8\times E_8$ string theory and are related to each other. In this case, dark photons can become a natural portal into the mirror world.

Unfortunately, the expected magnitude of the induced interactions of ordinary matter with mirror matter is too small to be of phenomenological interest.
Nonlinear polarizability of erythrocytes in non-uniform alternating electric field (NUAEF) was proved theoretically and experimentally by dielectrophoresis method.

The paper presents experimental evidence of the nonlinear polarizability of erythrocytes in the non-uniform alternating electric field. The rotation of erythrocyte around its own axis at more than one revolution per second in the non-uniform alternating electric field in the frequency range and the electric field intensity is the evidence of its nonlinear polarizability. The theoretical analysis of the density of electric charges capable of overcoming the membrane potential was carried out on the basis of statistical mechanics, the thermal equilibrium in which the particle stays.

The nonlinear polarizability of the erythrocyte emerges if the voltage on the membrane exceeds , which was theoretically proved. The alternating electric field from the donor erythrocyte with the amplitude exceeding forms the constant component of the current in the cytoplasm of the recipient erythrocyte whose energy can be considered as a signal one. The nonlinear equivalent electric circuit of the cell was proposed.
Новосибирский государственный университетЛексема «разум» как обозначение некоторых фрагментов семантического поля «интеллектуальная деятельность» в первом полном славянском переводе Корпуса Ареопагитик Рассматриваются лексико-семантические варианты лексемы ðàçîóìú в славянском переводе Корпуса Ареопагитик, выполненном во второй половине XIV в. на Афоне двуязычным сербским монахом и в его же предисловии к переводу.Лексема ðàçîóìú в переводе (201 словоупотребление) и оригинальном тексте переводчика, инока Исайи (2 словоупотребления), вербализует центральные элементы семантического поля «интеллектуальная деятельность», а именно «знание», «познание», «сознание, разум» (в порядке убывания).Критериями выделения отдельных лексико-семантических вариантов анализируемой лексемы были греческий эквивалент, показания микро-и макроконтекста, в некоторых случаях -современный перевод данного отрывка с греческого языка.В таком распределении лексико-семантических вариантов состоит отличие рассматриваемого идиолекта как от старославянского, так и от современного русского языка.
Microsatellite (SSR) markers with known precise intrachromosomal locations are widely used for mapping genes in rye and for the investigation of wheat-rye translocation lines and triticale highly demanded for mapping economically important genes and QTL-analysis. One of the sources of novel SSR markers in rye are microsatellites transferable from the wheat genome. Broadening the list of available SSRs in rye mapped to chromosomes is still needed, since some rye chromosome maps still have just a few microsatellite loci mapped.

The goal of the current study was to integrate wheat EST-SSRs into the existing rye genetic maps and to construct a consensus rye microsatellite map. Four rye mapping populations (P87/P105, N6/N2, N7/N2 and N7/N6) were tested with CFE (EST-SSRs) primers. A total of 23 Xcfe loci were mapped on rye chromosomes: Xcfe023, -136 and -266 on chromosome 1R, Xcfe006, -067, -175 and -187 on 2R, Xcfe029 and -282 on 3R, Xcfe004, -100, -152, -224 and -260 on 4R, Xcfe037, -208 and -270 on 5R, Xcfe124, -159 and -277 on 6R, Xcfe010, -143 and -228 on 7R.

With the exception of Xcfe159 and Xcfe224, all the Xcfe loci mapped were found in orthologous positions considering multiple evolutionary translocations in the rye genome relative to those of common wheat. The consensus map was constructed using mapping data from the four bi-parental populations. It contains a total of 123 microsatellites, 12 SNPs, 118 RFLPs and 2 isozyme loci.
Influence of the metal core composition and geometry on the structure, spectroscopic properties and redox potentials was investigated for the first time for heterometallic (Re/Mo)6 octahedral clusters. The discrete anionic clusters [Re6-x Mox Se8 (CN)6 ]n- (x=2, 3; n=4, 5) were obtained as individual salts. Their isomeric composition and bond-length distribution were inspected using a combination of single-crystal X-ray structure analysis, NMR, EXAFS, and DFT calculations.