Hengzongshu/ArticleAgent huggingface dataset:
Autism spectrum disorder (ASD) has a strong and complex genetic component with an estimate of more than 1000 genes implicated cataloged in SFARI (Simon′s Foundation Autism Research Initiative) gene database. A significant part of both syndromic and idiopathic autism cases can be attributed to disorders caused by the mechanistic target of rapamycin (mTOR)-dependent translation deregulation.

We conducted gene-set analyses and revealed that 606 out of 1053 genes (58%) included in the SFARI Gene database and 179 out of 281 genes (64%) included in the first three categories of the database ('high confidence', 'strong candidate', and 'suggestive evidence') could be attributed to one of the four groups: 1. FMRP (fragile X mental retardation protein) target genes, 2. mTOR signaling network genes, 3. mTOR-modulated genes, 4. vitamin D3 sensitive genes. The additional gene network analysis revealed 43 new genes and 127 new interactions, so in the whole 222 out of 281 (79%) high scored genes from SFARI Gene database were connected with mTOR signaling activity and/or dependent on vitamin D3 availability directly or indirectly.

We hypothesized that genetic and/or environment mTOR hyperactivation, including provocation by vitamin D deficiency, might be a common mechanism controlling the expressivity of most autism predisposition genes and even core symptoms of autism.
Objectives: The microbiome of sputum from former and active coal miners diagnosed with coal worker’s pneumoconiosis (CWP) as compared to healthy controls Methods: Next Generation Sequencing of bacterial 16S rRNA genes obtained from the sputum of CWP subjects.Results: Differences were detected between the sputum microbiomes from the healthy and CWP subjects. We noted a significant decrease in Bacteroidetes and an increase in the level of Proteobacteria.Conclusions: The microbiomes found in sputum from CWP subjects are enriched in bacterial species previously reported to induce pro-inflammatory responses. The profile of the microbiomes correlated mainly to the occupational activity and not to the age of the coal miners.
One of the modern radiobiological problems is to estimate risks of chromosomal instability (RChI) for people and ecological populations located near the radiation sources. Our aim was to work out the probability model of adaptation to estimate risks of chromosomal instability. Methods and Objectives. We used data on numbers of cells with abnormalities (CAs) in meristem of seeds seedling of plantain (Plantago major) growing in 30-km zone of NPP [Korogodina and Florko, NATO Proceedings, 2007] and frequency of CAs of blood lymphocytes of people living in radiation-polluted Tyumen and Irkutsk regions [Osipova et al, 2004]. Cytogenetic analyses were provided by standard methods. Model. Assumptions: a primary cells damaging induces a secondary one; the latter is accompanied by natural selection of cells and organisms. In mathematical term: both the primary and secondary damaging can be described by Poisson (P) law and selection by geometrical (G) one [Florko, Korogodina, 2007]. The total process can be described by P+G model. Results. It was shown that the distribution of seeds on the number of CAs should be P+G distributions. G-contribution (it is RChI) and therefore seeds survival are decreased dramatically near the NPP (up to 2 and 20% respectively). In addition to P- and G- distribution, a lognormal (LN) law can be revealed when we consider a distribution of persons on the CA frequencies because CA frequency depends on proliferate activity also. We considered samplings of persons who were irradiated directly through nuclear fall-out, their children and grant-children. It was shown that samplings of persons living in North Tyumen region are P+G-distributed, and G-contribution (RChI) decreases across the generations from 100 to 50%. Perhaps, G-law contributes constantly there due to food chain moss-deer-man. In Irkutsk region, interchange of G-, LN- and P- laws across the generation was observed. We can presume that the first generation was characterized by CAs originated from bystander effects (RChI~90%), the second one by inherited CAs proliferation, and the third one by CAs spontaneous level. Conclusion. G-parameters characterize the secondary processes of chromosomal instability and are very sensitive to irradiation intensity. They can be used to estimate the risks of chromosomal instability.
Thiophene-phenylene co-oligomers (TPCOs) are among the most promising materials for organic light emitting devices. Here we report on record high among TPCO single crystals photoluminescence quantum yield reaching 60%. The solution-grown crystals are stronger luminescent than the vapor-grown ones, in contrast to a common believe that the vapor-processed organic electronic materials show the highest performance. We also demonstrate that the solution-grown TPCO single crystals perform in organic field effect transistors as good as the vapor-grown ones. Altogether, the solution-grown TPCO crystals are demonstrated to hold great potential for organic electronics.
We study the nonlinear stage of the modulation instability of a condensate in the framework of the focusing nonlinear Schrödinger equation (NLSE). We find a general N-solitonic solution of the focusing NLSE in the presence of a condensate by using the dressing method. We separate a special designated class of "regular solitonic solutions" that do not disturb phases of the condensate at infinity by coordinate. All regular solitonic solutions can be treated as localized perturbations of the condensate. We find an important class of "superregular solitonic solutions" which are small perturbations at a certain moment of time. They describe the nonlinear stage of the modulation instability of the condensate.
Scientists and laymen alike have always been fascinated by the ability of lenses and mirrors to control light. Now, with the advent of metamaterials and their two-dimensional counterpart metasurfaces, such components can be miniaturized and designed with additional functionalities, holding promise for system integration.

To demonstrate this potential, here ultrathin reflection metasurfaces (also called metamirrors) designed for focusing terahertz radiation into a single spot and four spaced spots are proposed and experimentally investigated at the frequency of 0.35 THz. Each metasurface is designed using a computer-generated spatial distribution of the reflection phase. The phase variation within 360 deg is achieved via a topological morphing of the metasurface pattern from metallic patches to U-shaped and split-ring resonator elements, whose spectral response is derived from full-wave electromagnetic simulations.

The proposed approach demonstrates a high-performance solution for creating low-cost and lightweight beam-shaping and beam-focusing devices for the terahertz band.
Apoptosis plays a crucial role in chemotherapy-induced cell death. The conventional theory holding that apoptosis needs to be immunologically silent has recently been revised, and the concept of immunogenic cell death (ICD) has been proposed.

This review describes the main features of ICD induction. These ICD markers are important for the effectiveness of anticancer therapy, as well as for basic research into cell death regulation. The mechanism of the vaccination effect of dying cancer cells undergoing ICD has been fully described, including the activation of specific antitumor response after re-challenge by the same living tumor cells. This review also discusses the whole set of molecular events attributing cell death to immunogenic type: the exposure of calreticulin and the heat shock protein HSP70 to the outer surface of the cell membrane and the release of the nuclear protein HMGB1 and ATP into the extracellular space.

ICD inducers of various nature (chemotherapy drugs, cytotoxic proteins, and oncolytic viruses), as well as physical methods, are classified in the current review.
ApoE expression status was proved to be a highly specific marker of energy metabolism rate in the brain. Along with its neighbor, Translocase of Outer Mitochondrial Membrane 40 kDa (TOMM40) which is involved in mitochondrial metabolism, the corresponding genomic region constitutes the neuroenergetic hotspot.

Using RNA-Seq data from a murine model of chronic stress a significant positive expression coordination of seven neighboring genes in ApoE locus in five brain regions was observed. Correlation analysis revealed a close association of ApoE and proopiomelanocortin (Pomc) gene expression profiles.

ApoE maintains one of the highest absolute expression values genome-wide, implying that ApoE can be the driver of the neighboring gene expression alteration observed under stressful loads. Notably, we revealed the highly statistically significant increase of ApoE expression in the hypothalamus of chronically aggressive (FDR < 0.007) and defeated (FDR < 0.001) mice compared to the control. implying the putative neuroendocrine stress response background of ApoE expression elevation therein.
A molecular mechanism of somaclonal variation is proposed

Oxidative stress caused by altered oxygen regime, the disturbance of the normal antioxidant status and the presence of strong prooxidants in cell culturing media are suggested to be the main reasons of the variations. Primary, secondary and final products of lipid peroxidation caused by oxidative stress can be directly responsible for plant genome instability.

The proposed mechanism of somaclonal variation could be the basis for development of new biotechnological approaches to this process.
Maturity onset diabetes of the young (MODY) is a congenital form of diabetes characterized by onset at a young age and a primary defect in pancreatic-β-cell function. Currently, 14 subtypes of MODY are known, and each is associated with mutations in a specific gene: HNF4A, GCK, HNF1A, PDX1, HNF1B, NEUROD1, KLF11, CEL, PAX4, INS, BLK, KCNJ11, ABCC8, and APPL1. The most common subtypes of MODY are associated with mutations in the genes GCK, HNF1A, HNF4A, and HNF1B. Among them, up to 70% of cases are caused by mutations in GCK and HNF1A.

Here, an analysis of 14 MODY genes was performed in 178 patients with a MODY phenotype in Western Siberia. Multiplex ligation-dependent probe amplification analysis of DNA samples from 50 randomly selected patients without detectable mutations did not reveal large rearrangements in the MODY genes.

In 38 patients (37% males) among the 178 subjects, mutations were identified in HNF4A, GCK, HNF1A, and ABCC8. We identified novel potentially causative mutations p.Lys142*, Leu146Val, Ala173Glnfs*30, Val181Asp, Gly261Ala, IVS7 c.864 −1G>T, Cys371*, and Glu443Lys in GCK and Ser6Arg, IVS 2 c.526 +1 G>T, IVS3 c.713 +2 T>A, and Arg238Lys in HNF1A.
We prove that the dimension of trivariate tensor-product spline space of tri-degree (m,m,m) with maximal order of smoothness over a three-dimensional domain coincides with the number of tensor-product B-spline basis functions acting effectively on the domain considered. A domain is required to belong to a certain class. This enables us to show that, for a certain assumption about the configuration of a hierarchical mesh, hierarchical B-splines span the spline space. This paper presents an extension to three-dimensional hierarchical meshes of results proposed recently by Giannelli and Jüttler for two-dimensional hierarchical meshes.
Two binuclear coordination compounds of Cu(II) chloride with the bitopic ligand 1,1,2,2-tetrakis(pyrazol-1-yl)ethane (Pz4) of the composition [Cu2(µ2-Pz4)(DMSO)2Cl4]·4H2O and [Cu2(µ2-Pz4)(DMSO)2Cl4]∙2DMSO were prepared and characterized by elemental analysis, IR spectroscopy, thermogravimetric analysis, single-crystal X-ray diffraction, and powder diffraction analysis. It was shown that in contrast to silver(I) and copper(II) nitrates, copper(II) chloride forms discrete complexes instead of coordination polymers. The supramolecular structure of the complex [Cu2(µ2-Pz4)(DMSO)2Cl4]·4H2O with lattice water molecules is formed by OH···Cl and OH···O hydrogen bonds. Density functional theory (DFT) calculations of vibrational frequencies of the ligand and its copper(II) complex allowed for assigning IR bands to specific vibrations.
In this work we generalize the classical framework of Mueller (or amplitude) scattering matrices for the Bessel beams (BBs). For that we extend the rotation relations of BBs (considering 'vortex' additional phase factor) for an arbitrary angle, which are useful for solving the scattering problem in a rotated coordinate system. Thus, we rework the existing classification of the BBs and their polarizations with the focus on rotation relations between them. We have already implemented all BB types with arbitrary polarizations/rotations in a separate branch of ADDA, and are working on testing the code. As a result, it should be trivial for anyone to simulate the scattering of Bessel beams by arbitrary inhomogeneous particles, including randomly orientated ones.
The fruit fly Drosophila melanogaster is a classic research object in genetics and systems biology. In the genetic analysis of flies, a routine task is to determine the offspring size and gender ratio in their populations. Currently, these estimates are made manually, which is a very time-consuming process.

The counting and gender determination of flies can be automated by using image analysis with deep learning neural networks on mobile devices. We proposed an algorithm based on the YOLOv4-tiny network to identify Drosophila flies and determine their gender based on the protocol of taking pictures of insects on a white sheet of paper with a cell phone camera. Three strategies with different types of augmentation were used to train the network.

The best performance (F1 = 0.838) was achieved using synthetic images with mosaic generation. Females gender determination is worse than that one of males. Among the factors that most strongly influencing the accuracy of fly gender recognition, the fly’s position on the paper was the most important. Increased light intensity and higher quality of the device cameras have a positive effect on the recognition accuracy. We implement our method in the FlyCounter Android app for mobile devices, which performs all the image processing steps using the device processors only. The time that the YOLOv4-tiny algorithm takes to process one image is less than 4 s.
The dynamics of explosive vaporization of the 2-propanol/water and ethanol/ water mixtures on the multilayer thin-film resistor with the size of 100×110 m has been investigated.

An original optical method based on measuring the laser intensity reflected from resistor surface was used.

The characteristics of the initial stage of the explosive vaporization of two-component mixtures were obtained. The dependence of the temperature of explosive vaporization on the rate of temperature growth and the dependence of the boiling time on effective heat flux were defined.
We present an algorithm for detecting metaphor in sentences which was used in Shared Task on Metaphor Detection by First Workshop on Figurative Language Processing. The algorithm is based on different features and Conditional Random Fields.
In wheat, anthocyanin pigments can be accumulated in pericarp tissues (under control of the Pp genes) resulting in purple-colored grain.

In the current study, a strategy, based on the use of molecular and morphological markers, was applied to create purple-grained bread wheat cultivars adapted to the West Siberian region. The breeding scheme started from crossing of recipients (elite cultivars and lines) with donor lines carrying dominant alleles of the complementary genes Pp3 and Pp-D1. The F2 hybrids passed three-step marker-assisted selection, and those having dominant Pp-D1Pp-D1Pp3Pp3 genotypes were backcrossed with the recurrent parents. The desired BC1F2-3 progenies were selected using morphological marker, while BC1F3 also passed through field evaluation. At this stage, 120 lines were selected and planted in individual 1 m2 'breeding nursery (BN) plots' for assessment of heading dates, duration of vegetation period, resistance to powdery mildew, stem and leaf rusts, protein and gluten content, as well as productivity.

After these investigations, a total of 17 promising anthocyanin-rich purple-grained lines characterized by multiple resistance and having best yield/quality characteristics were finally candidates for selection of commercial cultivars adapted to the West Siberian climate and suitable for functional food production.
Old analog and modern systems with digital signal processing are analyzed using active field control (AFC). The AFC3 system from Yamaha, Moscow, Russia, installed in the Great Hall of the Tyumen Philharmonic is considered.

The diagrams of early reflections are obtained by computer acoustical simulation of the Great Hall. The control measurement results confirm the effectiveness of the proposed solutions.

The intrinsic reverberation time is 1.1 s. The AFC3 system provides the increase in the reverberation time up to 2.65 s. For the first time in Russia, the electronic shell is constructed for the fly-loft stage in the Tyumen Philharmonic, that allows improving the acoustical conditions for musicians.
The measurement is based on the final Belle data sample of 976/fb.

The results are y_CP=(1.11 +- 0.22 +- 0.09)% and A_Gamma=(-0.03 +- 0.20 +- 0.07)%, where the first uncertainty is statistical and the second is systematic.
We consider a resource-constrained project scheduling problem with respect to the makespan minimization criterion. The problem accounts for technological constraints of activities precedence together with resource constraints. Activities pre- emptions are not allowed. The problem with renewable resources is NP-hard in the strong sense. We propose an exact branch and bound algorithm for solving the problem with renewable resources. It uses our new branching scheme based on the representation of a schedule in form of the activity list. We use two approaches of constructing the lower bound. We present results of numerical experiments, illustrating the quality of the proposed lower bounds. The test instances are taken from the library of test instances PSPLIB.
Signal Amplification by Reversible Exchange (SABRE) is a promising method for NMR signal enhancement and production of hyperpolarized molecules. As nuclear spin relaxation times of heteronuclei are usually much longer than those of protons, SABRE‐based hyperpolarization of heteronuclei in molecules is highly important in the context of biomedical applications. In this work, we demonstrate that the SLIC‐SABRE technique can be successfully used to hyperpolarize 15 N nuclei in dalfampridine. The high polarization level of ca. 8 % achieved in this work made it possible to acquire 15 N MR images at natural abundance of the 15 N nuclei for the first time.
Two tests are described that were developed for benchmarking and comparison of numerical codes in the context of AWAKE experiment.
The evolution of eukaryotes is one of the most important issues in the history of life. Paleontological studies discovered the oldest eukaryotic fossil from the Paleoproterozoic Francevillian Group in Gabon.

To clarify specific features of ancient sedimentary basins in Gabon, geologic evidence for the Francevillian Group is summarized and a new geotectonic model is proposed. The model gives much weight to the upwelling of mantle plume, which can explain why the Francevillian basin only hosted natural reactors.

The Great Oxidation Event in the Paleoproterozoic played an important role in not only the evolution of eukaryotes but also in the formation of natural reactors. Reductive weathering of the continental crust, which was affected by plume-related volcanisms, transported Uranium-rich minerals into sediments of the Francevillian Group without dissolution of Uranium. The subsequent oxidation event enabled uranyl ions to accumulate within an oxic failed rift basin, and settled large quantities of organic matter on the seafloor. Hydrothermal circulation within the Francevillian Group precipitated highly Uranium-rich ores, which became natural reactors at approximately 2.0 Ga, and might have influenced the evolution of eukaryotes in this basin. In a large sense, the degree of oxidation of the ocean-atmosphere system has been linked to the amount of sedimentary rocks. In that way, mantle overturn in 2.7 Ga, which created a large continental crust, was one of the crucial events that affected the evolution of eukaryotes.
Efficient oxygen transfer through Me–CeO2 interface explains higher activity of MeOx/CeO2 (Me = Fe, Co, Ni) samples in deN2O and NH3 oxidation compared with MeOx/Al2O3 ones.
Cerebral arteriovenous malformation (AVM) is a congenital brain vessels pathology, in which the arterial and venous blood channels are connected by tangles of abnormal blood vessels. It is a dangerous disease that affects brain functioning causing the high risk of intracerebral haemorrhage. One of AVM treatment methods is embolization—the endovascular filling of the AVM vessel bundle with a special embolic agent. This method is widely used, but still in some cases is accompanied by intraoperative AVM vessels rupture. In this paper, the optimal scenario of AVM embolization is studied from the safety and effectiveness of the procedure point of view. The co-movement of blood and embolic agent in the AVM body is modelled on the basis of a one-dimensional two-phase filtration model. Optimal control problem with phase constraints arising from medicine is formulated and numerically solved. In numerical analysis, the monotone modification of the CABARET scheme is used. Optimal embolization model is constructed on the basis of real patients' clinical data collected during neurosurgical operations. For the special case of embolic agent, input admissible and optimal embolization scenarios were calculated.
Currently, the detection of the allele asymmetry of gene expression from RNA-seq data or the transcription factor binding from ChIP-seq data is one of the approaches used to identify the functional genetic variants that can affect gene expression (regulatory SNPs or rSNPs). In this study, we searched for rSNPs using the data for human pulmonary arterial endothelial cells (PAECs) available from the Sequence Read Archive (SRA). Allele-asymmetric binding and expression events are analyzed in paired ChIP-seq data for H3K4me3 mark and RNA-seq data obtained for 19 individuals. Two statistical approaches, weighted z-scores and predicted probabilities, were used to improve the efficiency of finding rSNPs. In total, we identified 14,266 rSNPs associated with both allele-specific binding and expression. Among them, 645 rSNPs were associated with GWAS phenotypes; 4746 rSNPs were reported as eQTLs by GTEx, and 11,536 rSNPs were located in 374 candidate transcription factor binding motifs. Additionally, we searched for the rSNPs associated with gene expression using an SRA RNA-seq dataset for 281 clinically annotated human postmortem brain samples and detected eQTLs for 2505 rSNPs. Based on these results, we conducted Gene Ontology (GO), Disease Ontology (DO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses and constructed the protein–protein interaction networks to represent the top-ranked biological processes with a possible contribution to the phenotypic outcome.