Hengzongshu/ArticleAgent huggingface dataset:
The development of quantitative digital phenotyping methods for evaluation of wild potato (section Petota Dumort., genus Solanum L.) tuberization is required for annotation of genebank collections and selection of the suitable donor material for potato breeding. There are no available methods specifically designed for the quantitative analysis of wild potato tuber morphology. The current study is devoted to evaluation of wild potato tubers’ morphological characteristics using a digital image processing technique. For this purpose, the mobile application SeedSounter developed previously for grain analysis was specifically adapted for tuber phenotyping. The application estimates the number and shape of objects scattered on a standard sheet of white paper (i. e. A3 or A4). Twelve accessions from the VIR genebank collection belonging to nine Petota species were grown in pots protected with garden fabric during the growing season of cultivated potato (Novosibirsk region). Tubers were collected form plants of nine genotypes. Three genotypes did not produce tubers. The weight of tubers collected from each plant was measured. The tuber yield from each plant was analyzed using SeedCounter (http://wheatdb.org/seedcounter). The number of tubers per plant was counted; the following characteristics were extracted from the images of individual tubers: length, width, projected area, length to width ratio, сircularity, roundness, rugosity and solidity. One-way ANOVA showed a significant effect of genotype on all measured characteristics. A pairwise comparison of nine Petota accessions using all measured parameters revealed statistically significant differences between 86 % of pairs. The overall tuber yield volume for each plant was calculated as a sum of volumes of individual tubers; tuber volume was calculated from its length to width ratio and projected area. A strong correlation between the evaluated tuber yield volume and yield weight was shown. We propose tuber yield volume as a characteristic for a general evaluation of tuberization for wild potato, implementing the four-step scale from 0 to 3. According to this characteristic, the twelve wild potato accessions studied could be divided into four groups with different tuberization abilities. The evaluated tuberization ability is partially in accordance with previously obtained VIR data. The results presented demonstrate the possibility to use SeedCounter for wild potato collections phenotyping.
Aim . To study APOA5 genetic polymorphism in Caucasoid patients with familial hypercholesterolemia. Methods . Sample of patient with familial hypercholesterolemia (43 unrelated Caucasoid persons) was formed using Dutch Lipid Clinic Network Criteria. Targeted sequencing of genome DNA was performed by NimbleGen SeqCap EZ Choice kit on pyrosequencer Roche Junior GS (Roche, Switzerland). Results . In patients with familial hypercholesterolemia, 8 substitutions were identified in the APOA5 gene: rs2075291, rs3135506, rs2072560, rs2266788, rs3135507, rs34089864, rs619054, and rs651821, that are known to be associated with dyslipidemia. One novel substitution Ala169Asp was found. It is responsible for changing the charge of a domain for lipid droplets binding in the APOA5 protein. There were no differences in the frequencies of the ApoA5*2 intragenic haplotype, which has been recently reported to be associated with an increased triglyceride levels in patients with familial hypercholesterolemia and the population. Conclusion. Genetic variants ofAPOA5, common in patients with familial hypercholesterolemia, may be involved in the formation of the pathological phenotype of dyslipidemia. However, a more accurate assessment oftheir contribution is required to differentiate patients with familial hypercholesterolemia according to their triglycerides level.
Timed transition systems are a widely studied model for real-time systems.

The intention of the paper is to show how several categorical (open maps, path-bisimilarity and coalgebraic) approaches to an abstract characterization of bisimulation relate to each other

and to the numerous suggested behavioral equivalences of linear time -- branching time spectrum, in the setting of timed transition systems.
Interaction of ultrashort laser pulses with transparent materials is a powerful technique of modification of material properties for various technological applications. The physics behind laser-induced modification phenomenon is rich and still far from complete understanding.

We present an overview of our models developed to describe processes induced by ultrashort laser pulses inside and on the surface of bulk glass. The most sophisticated model consists of two parts. The first part solves Maxwell's equations supplemented by the rate and hydrodynamics equations for free electrons. The model resolves spatiotemporal dynamics of free-electron population and yields the absorbed energy map. The latter serves as an initial condition for thermoelastoplastic simulations of material redistribution. To gain insight into temperature evolution of a glass material under the surface irradiation conditions, we employ a model based on the rate equation describing free electron generation coupled with the energy equations for electrons and lattice. Finally, a model is outlined, developed for multi-pulse irradiation regimes, which enables gaining insight into the roles of defects and heat accumulation.

The simulations performed for a wide range of irradiation conditions have allowed to clarify timescales at which modification occurs after single laser pulses. Simulations of spectrum of laser light scattered by laser-generated plasma revealed considerable blueshifting which increases with pulse energy. Swift heating of electron and lattice subsystems to extremely high temperatures at fs timescale has been found at laser fluences exceeding the threshold fluence by 2-3 times that can result in efficient bremsstrahlung emission from the irradiation spot. The mechanisms of glass ablation with ultrashort laser pulses are discussed by comparing with the experimental data.
The purpose of the study was to analyze the antitumor effects of the extract of mycelium from Duddingtonia flagrans (strain F-882) on xenografts of human C33a cervical cancer cells.

Material and Methods. To evaluate the antitumor effect, we used the absolute values of xenograft volumes and calculated the tumor growth inhibition and the index of tumor growth. Results . At the first stage of the experiment, a 4-week subcutaneous injection of the water extract of F-882 resulted in an almost twofold slowdown in xenograft growth, with the tumor growth inhibition value of 50.6 %. In the second stage of the experiment, a 2.5-week subcutaneous injection followed by a 1.5-week intratumoral injection of F-882 also caused the tumor growth inhibition. After completing F-882 injections, the effect of tumor growth inhibition continued for 2.5 weeks and the tumor growth inhibition value was 58.7 %.

Conclusion. The mycelium extract F-882 was shown to have an antitumor effect on subcutaneous xenografts of human C33a cervical carcinoma cells.
Siberia is one of the coldest environments on Earth and has great seasonal temperature variation. Long-term settlement in northern Siberia undoubtedly required biological adaptation to severe cold stress, dramatic variation in photoperiod, and limited food resources. In addition, recent archeological studies show that humans first occupied Siberia at least 45,000 years ago; yet our understanding of the demographic history of modern indigenous Siberians remains incomplete.

In this study, we use whole-exome sequencing data from the Nganasans and Yakuts to infer the evolutionary history of these two indigenous Siberian populations. Recognizing the complexity of the adaptive process, we designed a model-based test to systematically search for signatures of polygenic selection. Our approach accounts for stochasticity in the demographic process and the hitchhiking effect of classic selective sweeps, as well as potential biases resulting from recombination rate and mutation rate heterogeneity.

Our demographic inference shows that the Nganasans and Yakuts diverged ∼12,000-13,000 years ago from East-Asian ancestors in a process involving continuous gene flow. Our polygenic selection scan identifies seven candidate gene sets with Siberian-specific signals. Three of these gene sets are related to diet, especially to fat metabolism, consistent with the hypothesis of adaptation to a fat-rich animal diet. Additional testing rejects the effect of hitchhiking and favors a model in which selection yields small allele frequency changes at multiple unlinked genes.
Spatial distributions of positively charged species naturally occurring in the stoichiometric and fuel-rich premixed H2/CO/O2/Ar flames are measured with molecular beam mass spectrometry. The hydronium (H3O+) ion and its clusters are found to be most abundant cations in the flames. The ion chemistry model proposed earlier by Belhi et al. (2018) for lean methane flames is validated against the measurement data. The model was found to adequately predict the observed tendencies in the flames, once the exact mixture composition, including hydrocarbon impurities (∼5 ppm), is considered.
The three-dimensional dynamics of droplets on inclined and vertical walls in a gravity field is simulated. The dependence of a contact angle on a velocity of contact line is obtained for slow regime and smooth surface.

The simulations of a rupture of the liquid films on the nonwettable solid substrate due to the thermocapillary effect (Marangoni effect) are also carried out.

The lattice Boltzmann method is successfully implemented for computer simulation of these three-dimensional problems.
An isoquinoline alkaloid berberine and its derivatives exhibit a wide range of biological activities including antibacterial, hypolipidemic, anticancer and other properties. We have shown for the first time that berberine derivatives are effective inhibitors of the human DNA repair enzyme tyrosyl-DNA phosphodiesterase (Tdp1), which opens the possibility to use them as an adjuvant component of chemotherapy. We synthesised and analysed a few different types of berberine derivatives and studied their inhibitory activity. Berberine-based sulfonates and sultones have been shown to exhibit high inhibitory activity against Tdp1. This work was supported by Russian Science Foundation (grant 19-13-00040)
The gasification of Russian regions is one of the most important problems for the national economy. The development of the gas supply system contributes to the socio-economic development of the regional economy, to the increase increasing the level and quality of life, and to the solution of the key environmental issues. The Krasnoyarskiy Kray is the only region in the east of the country that has a significant resource potential of natural gas but at the same time, it can’t be connected to the trunk gas pipeline in the short and long term perspective. The purpose of the study is to assess the efficiency of investments in the construction of gas supply facilities, gasification, and their exploitation in the southern and central regions of the Krasnoyarskiy Kray. In this study authors solved the following objectives: we systematized information about the current state of the Krasnoyarskiy Kray gasification and the prerequisites for its development (resource base and transport infrastructure); we assessed economic efficiency of the investments in the construction, gasification, and exploitation of gas supply facilities in the southern and central regions of the Krasnoyarskiy Kray; we formulated proposals to ensure economic efficiency using the mechanism of public-private partnership. The authors recommend an option according to which federal budget investments will amount to 70% of their total investment in the Krasnoyarskiy Kray gasification program. Under this option, the selling price of gas will drop to 4708 rubles per 1000 cubic meters of natural gas excluding VAT. Organization of production, preparation for transport, and transportation of natural gas in the central regions of the Krasnoyarskiy Kray will create new highly paid jobs, significantly increase the GRP, and improve the demographic situation.
Cardiac hypertrophy accompanies many forms of cardiovascular diseases. The mechanisms behind the development and regulation of cardiac hypertrophy in the human setting are poorly understood, which can be partially attributed to the lack of a human cardiomyocyte-based preclinical test system recapitulating features of diseased myocardium.

The objective of our study is to determine whether human embryonic stem cell-derived cardiomyocytes (hESC-CMs) subjected to mechanical stretch can be used as an adequate in vitro model for studying molecular mechanisms of cardiac hypertrophy. We show that hESC-CMs subjected to cyclic stretch, which mimics mechanical overload, exhibit essential features of a hypertrophic state on structural, functional, and gene expression levels.

The presented hESC-CM stretch approach provides insight into molecular mechanisms behind mechanotransduction and cardiac hypertrophy and lays groundwork for the development of pharmacological approaches as well as for discovering potential circulating biomarkers of cardiac dysfunction.
In this work modern methods of investment project efficiency evaluation were studied, advantages and disadvantages of using the real option model were shown in comparison with the DCF model. It is proved that a rainbow option is an effective valuation tool in conditions of high oil prices volatility and low study of reserves and resource. Two stages may be identified: mineral exploration and maintenance work. Black-Scholes model was used for option pricing.
Anthocyanins and melanins are phenolic pigments of plants and accumulate in seed envelopes of the barley grain, thereby giving them a blue, purple, or black color.

To explore the effects of combined accumulation of anthocyanins and melanins in the grain, a barley near-isogenic line (NIL), characterized by simultaneous accumulation in both pigments, was developed using a marker-assisted approach. The presence of both pigments in the grain pericarp was evaluated by light microscopy.

Emergence of anthocyanin pigmentation proved to be temporally separated from that of melanin, and the formation of anthocyanin pigments began at an earlier stage of spike maturation. During spike maturation, a significantly higher total anthocyanin content was noted in the created NIL than in the parental anthocyanin-accumulating NIL, indicating a positive influence of the Blp1 gene on the anthocyanin content at some developmental stages. In a comparative analysis of yield components, it was found that the observed differences between the barley NILs are possibly caused by environmental factors, and the presence of pigments does not decrease plant productivity. Our results should facilitate investigation into genetic mechanisms underlying overlaps in the biosynthesis of pigments and into breeding strategies aimed at the enrichment of barley varieties with polyphenols.
There are many available software tools for visualization and analysis of biological networks. Among them, Cytoscape ( http://cytoscape.org/ ) is one of the most comprehensive packages, with many plugins and applications which extends its functionality by providing analysis of protein-protein interaction, gene regulatory and gene co-expression networks, metabolic, signaling, neural as well as ecological-type networks including food webs, communities networks etc. Nevertheless, only three plugins tagged 'network evolution' found in Cytoscape official app store and in literature. We have developed a new Cytoscape 3.0 application Orthoscape aimed to facilitate evolutionary analysis of gene networks and visualize the results. Orthoscape aids in analysis of evolutionary information available for gene sets and networks by highlighting: (1) the orthology relationships between genes; (2) the evolutionary origin of gene network components; (3) the evolutionary pressure mode (diversifying or stabilizing, negative or positive selection) of orthologous groups in general and/or branch-oriented mode. The distinctive feature of Orthoscape is the ability to control all data analysis steps via user-friendly interface. Orthoscape allows its users to analyze gene networks or separated gene sets in the context of evolution. At each step of data analysis, Orthoscape also provides for convenient visualization and data manipulation.
Universal enveloping commutative Rota–Baxter algebras of pre- and post-commutative algebras are constructed. The pair of varieties (RBλCom, postCom) is proved to be a Poincaré–Birkhoff–Witt-pair (PBW)-pair and the pair (RBCom, preCom) is proven not to be.
At present time Budker INP is developing a Super Charm-Tau factory project, which consists of a high-luminosity collider with the luminosity of 1035 cm−2s−1 and a universal magnetic detector. The tracking system of the detector will comprise of an Inner Tracker (IT) and a Drift Chamber (DC). One of the options for IT is Time Projection Chamber (TPC). The advantages of the TPC are high spatial resolution and particle identification capabilities by registration of dE/dx losses. However, using a Time Projection Chamber implies serious challenges. For example, the TPC have to simultaneously deal with tracks from several thousands events and maintain the enormous data rate.

This work describes the results of the Monte-Carlo studies of the transport characteristics in various gas mixtures proposed for TPC.

Besides of this, the simulation of the ion back flow and its effect on spatial resolution will be reported.
Ultrasound assessment of myocardial strain allows non-invasive identification of early stages of heart failure with preserved ventricular ejection fraction. A decline of the left ventricle (LV) global longitudinal strain in hypertension (HT) accompanied by LV hypertrophy (LVH) was reported in clinical samples with manifest HT. Data on the relationship between longitudinal strain and blood pressure (BP) and HT in general population is lacking.

The cross-sectional study was based on a population cohort (HAPIEE, Novosibirsk). In a random sample (n = 416, aged 55–84 years old) we performed echocardiography and evaluated GLS and GSR of LV by speckle tracking technique. ANOVA multivariable models were applied.

In the studied population sample, GLS and GSR of LV were associated with HT; however, the association between GLS and HT was largely explained by BMI. In hypertensives, the lowest GLS and GSR, as well as higher extent of LVH, were found among those treated ineffectively, which might point at the initial reduction of systolic ventricular function in HT with inadequate BP control.
In the present paper we numerically study instrumental impact on statistical properties of quasi-CW Raman fiber laser using a simple model of multimode laser radiation. Effects, that have the most influence, are limited electrical bandwidth of measurement equipment and noise.

To check this influence, we developed a simple model of the multimode quasi-CW generation with exponential statistics (i.e. uncorrelated modes).

We found that the area near zero intensity in probability density function (PDF) is strongly affected by both factors, for example both lead to formation of a negative wing of intensity distribution. But far wing slope of PDF is not affected by noise and, for moderate mismatch between optical and electrical bandwidth, is only slightly affected by bandwidth limitation. The generation spectrum often becomes broader at higher power in experiments, so the spectral/electrical bandwidth mismatch factor increases over the power that can lead to artificial dependence of the PDF slope over the power. It was also found that both effects influence the ACF background level: noise impact decreases it, while limited bandwidth leads to its increase.
Study of the relationship between the structural and functional organization of proteins and their coding genes is necessary for an understanding of the evolution of molecular systems and can provide new knowledge for many applications for designing proteins with improved medical and biological properties. It is well known that the functional properties of proteins are determined by their functional sites. Functional sites are usually represented by a small number of amino acid residues that are distantly located from each other in the amino acid sequence. They are highly conserved within their functional group and vary significantly in structure between such groups. According to this facts analysis of the general properties of the structural organization of the functional sites at the protein level and, at the level of exon-intron structure of the coding gene is still an actual problem. One approach to this analysis is the projection of amino acid residue positions of the functional sites along with the exon boundaries to the gene structure.

In this paper, we examined the discontinuity of the functional sites in the exon-intron structure of genes and the distribution of lengths and phases of the functional site encoding exons in vertebrate genes. We studied the characteristics of the structure of the exon boundaries that code, and do not code, functional sites in 11 Metazoa species.

We have shown that the DNA fragments coding the functional sites were in the same exons, or in close exons. The observed tendency to cluster the exons that code functional sites which could be considered as the unit of protein evolution. This is accompanied by a reduced frequency of intercodon gaps (phase 0) in exons encoding the amino acid residue functional site, which may be evidence of the existence of evolutionary limitations to the exon shuffling. These results characterize the features of the coding exon-intron structure that affect the functionality of the encoded protein and allow a better understanding of the emergence of biological diversity.
Sensing infrared radiation is done inexpensively with pyroelectric detectors that generate a temporary voltage when they are heated by the incident infrared radiation. Unfortunately the performance of these detectors deteriorates for longer wavelengths, leaving the detection of, for instance, millimetre-wave radiation to expensive approaches. We propose here a simple and effective method to enhance pyroelectric detection of the millimetre-wave radiation by combining a compact commercial infrared pyro-sensor with a metasurface-enabled ultra-thin absorber, which provides spectrally- and polarization-discriminated response and is 136 times thinner than the operating wavelength. It is demonstrated that, due to the small thickness and therefore the thermal capacity of the absorber, the detector keeps the high response speed and sensitivity to millimetre waves as the original infrared pyro-sensor does against the regime of infrared detection. An in-depth electromagnetic analysis of the ultra-thin resonant absorbers along with their complex characterization by a BWO-spectroscopy technique is presented. Built upon this initial study, integrated metasurface absorber pyroelectric sensors are implemented and tested experimentally, showing high sensitivity and very fast response to millimetre-wave radiation. The proposed approach paves the way for creating highly-efficient inexpensive compact sensors for spectro-polarimetric applications in the millimetre-wave and terahertz bands.