Hengzongshu/ArticleAgent huggingface dataset:
The values z of many observable quantities in the Nature are determined at some discrete set of times tn, separated by a small interval Δt (which may also represent a coordinate, etc.). Let the z value in neighbour point tn+1 = tn + Δt be expressed by the evolution equation as as z(tn+1) ≡ z(tn + Δt) = f(z(tn)). This equation gives a discrete description of phenomenon. Considering phenomena at t ≪ Δt this equation is transformed often into the differential equation allowing to determine z(t) leading to continuous description. It is usually assumed that the continuous description describes correctly the main features of a phenomenon at values t ≫ Δt.
Tumors of the jaws may represent different human disorders and frequently associate with pathologic bone fractures. In this report, we analyzed two affected siblings from a family of Russian origin, with a history of dental tumors of the jaws, in correspondence to original clinical diagnosis of cementoma consistent with gigantiform cementoma (GC, OMIM: 137575). To date, autosomal-dominant mutations have been described in the ANO5 gene for gnathodiaphyseal dysplasia (GDD, OMIM: 166260) and multiple recessive mutations have been described in the gene for muscle dystrophies (OMIM: 613319, 611307); the same amino acid (Cys) at the position 356 is mutated in GDD.

Whole exome sequencing revealed the heterozygous missense mutation c.1067G > A (p.Cys356Tyr) in ANO5 gene in these patients.

These genetic data and similar clinical phenotypes demonstrate that the GC and GDD likely represent the same type of bone pathology. Our data illustrate the significance of mutations in single amino-acid position for particular bone tissue pathology. Modifying role of genetic variations in another gene on the severity of the monogenic trait pathology is also suggested. Finally, we propose the model explaining the tissue-specific manifestation of clinically distant bone and muscle diseases linked to mutations in one gene.
Numerous publications of Russian and Mongolian researchers report the only species Fragaria orientalis Losinsk to be typical for Mongolia. However, by generally accepted taxonomy of Fragaria genus, the species F. orientalis is a tetraploid (2 n =4 x =28) which occupies a small area within Eastern regions of Russia and North-Western China. To clarify the specific belonging of strawberry, 11 Fragaria samples were collected in Central, Northern and Eastern parts of Mongolia. Species were identified by morphological characters and molecular marker of alcohol dehydrogenase adh1 gene. The results of the specific belonging study in Fragaria samples reveal two diploid species F. viridis and F. mandshrica growing in Mongolia.
As the evolution of miRNA genes has been found to be one of the important factors in formation of the modern type of man

we performed a comparative analysis of the evolution of miRNA genes in two archaic hominines, Homo sapiens neanderthalensis and Homo sapiens denisova, and elucidated the expression of their target mRNAs in bain.A comparative analysis of the genomes of primates, including species in the genus Homo, identified a group of miRNA genes having fixed substitutions with important implications for the evolution of Homo sapiens neanderthalensis and Homo sapiens denisova. The mRNAs targeted by miRNAs with mutations specific for Homo sapiens denisova exhibited enhanced expression during postnatal brain development in modern humans. By contrast, the expression of mRNAs targeted by miRNAs bearing variations specific for Homo sapiens neanderthalensis was shown to be enhanced in prenatal brain development.

Our results highlight the importance of changes in miRNA gene sequences in the course of Homo sapiens denisova and Homo sapiens denisova evolution. The genetic alterations of miRNAs regulating the spatiotemporal expression of multiple genes in the prenatal and postnatal brain may contribute to the progressive evolution of brain function, which is consistent with the observations of fine technical and typological properties of tools and decorative items reported from archaeological Denisovan sites. The data also suggest that differential spatial-temporal regulation of gene products promoted by the subspecies-specific mutations in the miRNA genes might have occurred in the brains of Homo sapiens denisova and Homo sapiens neanderthalensis, potentially contributing to the cultural differences between these two archaic hominines.
Astrocytes and microglia are the first cells to react to neurodegeneration, e.g., in Alzheimer's disease (AD); however, the data on changes in glial support during the most common (sporadic) type of the disease are sparse.

Using senescence-accelerated OXYS rats, which simulate key characteristics of sporadic AD, and Wistar rats (parental normal strain, control), we investigated hippocampal neurogenesis and glial changes during AD-like pathology. Using immunohistochemistry, we showed that the early stage of the pathology is accompanied by a lower intensity of neurogenesis and decreased astrocyte density in the dentate gyrus. The progressive stage is concurrent with reactive astrogliosis and microglia activation, as confirmed by increased cell densities and by the acquisition of cell-specific gene expression profiles, according to transcriptome sequencing data. Besides, here, we continued to analyze the anti-AD effects of prolonged supplementation with mitochondria-targeted antioxidant SkQ1. The antioxidant did not affect neurogenesis, partly normalized the gene expression profile of astrocytes and microglia, and shifted the resting/activated microglia ratio toward a decrease in the activated-cell density.

In summary, both astrocytes and microglia are more vulnerable to AD-associated neurodegeneration in the CA3 area than in other hippocampal areas; SkQ1 had an anti-inflammatory effect and is a promising modality for AD prevention and treatment.
Kotlin is a statically typed programming language that supports object-oriented and functional programming. It supports JVM, JS and native platforms via LLVM (Kotlin / Native). The first two targets are backed with well-developed virtual machines that can perform advanced program optimizations at runtime. However, for native platforms, all optimizations must be performed at compile time. Currently Kotlin / Native lacks many optimizations, which is why the performance of the generated code is poor in many cases.

This paper describes a way to solve this problem by introducing an additional SSA-based intermediate representation and implementing escape analysis using it.

Experimental results have shown that this approach can significantly improve performance.
We report the first observations of the spin-singlet bottomonium states hb(1P) and hb(2P). The states are produced in the reaction e+e−→hb(nP)π+π− using a 121.4 fb−1 data sample collected at energies near the Υ(5S) resonance with the Belle detector at the KEKB asymmetric-energy e+e− collider. We determine M[hb(1P)]=(9898.2+1.1+1.0−1.0−1.1) MeV/c2 and M[hb(2P)]=(10 259.8±0.6+1.4−1.0) MeV/c2, which correspond to P-wave hyperfine splittings ΔMHF=(+1.7±1.5) and (+0.5+1.6−1.2) MeV/c2, respectively. The significances of the hb(1P) and hb(2P) are 5.5σ and 11.2σ, respectively. We find that the production of the hb(1P) and hb(2P) is not suppressed relative to the production of the Υ(1S), Υ(2S), and Υ(3S).Received 2 August 2011DOI:https://doi.org/10.1103/PhysRevLett.108.032001© 2012 American Physical Society
The red fox (Vulpes vulpes) demonstrates a variety of coat colors including platinum, a common phenotype maintained in farm-bred fox populations. Foxes heterozygous for the platinum allele have a light silver coat and extensive white spotting, whereas homozygosity is embryonic lethal.

Two KIT transcripts were identified in skin cDNA from platinum foxes. The long transcript was identical to the KIT transcript of silver foxes, whereas the short transcript, which lacks exon 17, was specific to platinum. The KIT gene has several copies in the fox genome: an autosomal copy on chromosome 2 and additional copies on the B chromosomes. To identify the platinum-specific KIT sequence, the genomes of one platinum and one silver fox were sequenced. A single nucleotide polymorphism (SNP) was identified at the first nucleotide of KIT intron 17 in the platinum fox. In platinum foxes, the A allele of the SNP disrupts the donor splice site and causes exon 17, which is part of a segment that encodes a conserved tyrosine kinase domain, to be skipped. Complete cosegregation of the A allele with the platinum phenotype was confirmed by linkage mapping (LOD 25.59). All genotyped farm-bred platinum foxes from Russia and the US were heterozygous for the SNP (A/G), whereas foxes with different coat colors were homozygous for the G allele.

Identification of the platinum mutation suggests that other fox white-spotting phenotypes, which are allelic to platinum, would also be caused by mutations in the KIT gene.
Mechanisms that ensure repair of double-strand DNA breaks (DSBs) are instrumental in the integration of foreign DNA into the genome of transgenic organisms. After pronuclear microinjection, exogenous DNA is usually found as a concatemer comprising multiple co-integrated transgene copies.

We injected mouse zygotes with a pool of linear DNA molecules carrying unique barcodes at both ends and obtained 10 transgenic embryos with 1–300 transgene copies. Sequencing the barcodes allowed us to assign relative positions to the copies in concatemers and detect recombination events that occurred during integration. Our barcoding approach, verified with Pacific Biosciences Single Molecule Real-Time (SMRT) long-range sequencing, documents high activity of homologous recombination after DNA microinjection.

Cumulative analysis of approximately 1,000 integrated copies reveals that over 80% of them underwent recombination when their linear ends were processed by synthesis-dependent strand annealing (SDSA) or double-strand break repair (DSBR). We also observed evidence of double Holliday junction (dHJ) formation and crossing over during the concatemer formations. Sequencing indels at the junctions between copies shows that at least 10% of DNA molecules introduced into the zygotes are ligated by non-homologous end joining (NHEJ).
The Dalitz plot distribution of ${B}^{0}\ensuremath{\rightarrow}{\overline{D}}^{0}{K}^{+}{\ensuremath{\pi}}^{\ensuremath{-}}$ decays is studied using a data sample corresponding to $3.0\text{ }\text{ }{\mathrm{fb}}^{\ensuremath{-}1}$ of $pp$ collision data recorded by the LHCb experiment during 2011 and 2012. The data are described by an amplitude model that contains contributions from intermediate ${K}^{*}(892{)}^{0}$, ${K}^{*}(1410{)}^{0}$, ${K}_{2}^{*}(1430{)}^{0}$ and ${D}_{2}^{*}(2460{)}^{\ensuremath{-}}$ resonances. The model also contains components to describe broad structures, including the ${K}_{0}^{*}(1430{)}^{0}$ and ${D}_{0}^{*}(2400{)}^{\ensuremath{-}}$ resonances, in the $K\ensuremath{\pi}$ S-wave and the $D\ensuremath{\pi}$ S- and P-waves. The masses and widths of the ${D}_{0}^{*}(2400{)}^{\ensuremath{-}}$ and ${D}_{2}^{*}(2460{)}^{\ensuremath{-}}$ resonances are measured, as are the complex amplitudes and fit fractions for all components included in the amplitude model. The model obtained will be an integral part of a future determination of the angle $\ensuremath{\gamma}$ of the Cabibbo-Kobayashi-Maskawa quark mixing matrix using ${B}^{0}\ensuremath{\rightarrow}D{K}^{+}{\ensuremath{\pi}}^{\ensuremath{-}}$ decays.
A search is presented for the pair production of heavy vectorlike quarks, $T\overline{T}$ or $B\overline{B}$, that decay into final states with jets and no reconstructed leptons. Jets in the final state are classified using a deep neural network as arising from hadronically decaying $W/Z$ bosons, Higgs bosons, top quarks, or background. The analysis uses data from the ATLAS experiment corresponding to $36.1\text{ }\text{ }{\mathrm{fb}}^{\ensuremath{-}1}$ of proton-proton collisions with a center-of-mass energy of $\sqrt{s}=13\text{ }\text{ }\mathrm{TeV}$ delivered by the Large Hadron Collider in 2015 and 2016. No significant deviation from the Standard Model expectation is observed. Results are interpreted assuming the vectorlike quarks decay into a Standard Model boson and a third-generation-quark, $T\ensuremath{\rightarrow}Wb,Ht,Zt$ or $B\ensuremath{\rightarrow}Wt,Hb,Zb$, for a variety of branching ratios. At 95% confidence level, the observed (expected) lower limit on the vectorlike $B$-quark mass for a weak-isospin doublet ($B$, $Y$) is 950 (890) GeV, and the lower limits on the masses for the pure decays $B\ensuremath{\rightarrow}Hb$ and $T\ensuremath{\rightarrow}Ht$, where these results are strongest, are 1010 (970) GeV and 1010 (1010) GeV, respectively.
Multiplex polymerase chain reaction (PCR) has multiple applications in molecular biology, including developing new targeted next-generation sequencing (NGS) panels.

We present NGS-PrimerPlex, an efficient and versatile command-line application that designs primers for different refined types of amplicon-based genome target enrichment. It supports nested and anchored multiplex PCR, redistribution among multiplex reactions of primers constructed earlier, and extension of existing NGS-panels. The primer design process takes into consideration the formation of secondary structures, non-target amplicons between all primers of a pool, primers and high-frequent genome single-nucleotide polymorphisms (SNPs) overlapping. Moreover, users of NGS-PrimerPlex are free from manually defining input genome regions, because it can be done automatically from a list of genes or their parts like exon or codon numbers.

Using the program, the NGS-panel for sequencing the LRRK2 gene coding regions was created, and 354 DNA samples were studied successfully with a median coverage of 97.4% of target regions by at least 30 reads. To show that NGS-PrimerPlex can also be applied for bacterial genomes, we designed primers to detect foodborne pathogens Salmonella enterica , Escherichia coli O157:H7, Listeria monocytogenes , and Staphylococcus aureus considering variable positions of the genomes.
Many studies have shown that dichlorodiphenyltrichloroethane (DDT) exposure raises breast cancer risk. Another insecticide with similar properties is endosulfan, which has been actively used in agriculture after DDT prohibition. Previously, we have identified some estradiol-, progesterone-, and testosterone-sensitive microRNAs (miRNAs, miRs). Because DDT and endosulfan have estrogenic, antiandrogenic, and antiprogesterone properties, we hypothesized that these miRNAs are affected by the insecticides.

We quantified relative levels of miRNAs and expression levels of their target genes in breast cancer MCF-7 cells treated with p,p'-DDT, o,p'-DDT, or endosulfan. We also quantified miR-19b expression, which, as previously shown, is regulated by estrogen.

Here, we observed that miR-19b expression increased in response not only to estradiol but also to testosterone and progesterone. Treatment of MCF-7 cells with p,p'-DDT or endosulfan decreased the protein levels of apoptosis regulators TP53INP1 and APAF1. In cells treated with o,p'-DDT, the TP53INP1 amount decreased after 24 h of incubation, but increased after 48 h of incubation with insecticide. OXTR expression, which is known to be associated with breast carcinogenesis, significantly diminished under the exposure of all insecticides. In cells treated with p,p'-DDT or o,p'-DDT, the observed changes were accompanied by alterations of the levels of hormone-responsive miRNAs: miR-324, miR-190a, miR-190b, miR-27a, miR-193b, and miR-19b.
Interactions of mantle silicates with subducted carbonates, sulfides, and sulfur-rich fluids are experimentally simulated in the olivine-ankerite-sulfur and olivine-ankerite-pyrite systems using a multi-anvil high-pressure split-sphere apparatus at 6.3 GPa and range of 1050–1550 °C.

Recrystallization of Fe,Ni-bearing olivine and ankerite in a sulfur melt was found to be accompanied by sulfidation of olivine and carbonate, involving partial extraction of metals, carbon, and oxygen into the melt, followed by the formation of pyrite (±pyrrhotite), diopside, and Fe-free carbonates. The main features of metasomatic alteration of Fe,Ni-olivine by a reduced sulfur fluid include: (i) a zonal structure of crystals (Fe-rich core, Mg-rich rim); (ii) inclusions of pyrite and pyrrhotite in olivine; (iii) certain Raman spectral characteristics of olivine. At T > 1350 °C, two immiscible melts, a predominantly sulfur melt with dissolved components (or a Fe–Ni–S–O melt) and a predominantly carbonate one, are generated. The redox interaction of these melts leads to the formation of metastable graphite (1350–1550 °C) and diamond growth (1550 °C).

The studied olivine-ankerite-sulfur and olivine-ankerite-pyrite interactions may be considered as the basis for simulation of metasomatic processes accompanied by the formation of mantle sulfides during subduction of crustal material to the silicate mantle.
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.
In this study, we developed a continuum theory of the charge transport in dielectrics by trapped electrons and holes, which takes into account two separate contributions of the current of trapped charge carriers: the drift part and the diffusion one. It was shown that drift current is mostly dominant in the bulk, while the diffusion one reaches significant values near contacts. A comparison with other theoretical models and experiments shows a good agreement. The model can be extended to two- and three-dimensional systems. The developed model, formulated in partial differential equations, can be numerically implemented in the finite element method code.
The thermal parameters of the phase transitions and transport properties of tetra-n-butylammonium (TBA) perchlorate (n-C4H9)4NClO4 (TBAClO4) were investigated. TBAClO4 has a polymorphous transition at 330 K and melts at 487 K. The structure of the high-temperature (HT) phase belongs to cubic symmetry and is similar to the HT phases of TBABF4 and TBAI salts. The conductivity parameters of the low-temperature and HT phases of TBAClO4 were determined from the Arrhenius plots. The thermodynamic parameters and transport properties of TBAClO4 were compared with those of other TBA salts having isostructural HT phases. The polymorphous phase transition entropy was found to correlate with the conductivity of HT phases of TBA salts; TBAClO4 has the lowest conductivity compared to TBABF4 and TBAI salts.
The formation of hybrid sterility is an important stage of speciation. The voles of the genus Microtus , which is the most speciose genus of rodents, provide a good model for studying the cytological mechanisms of hybrid sterility. The voles of the “ mystacinus ” group of the subgenus Microtus (2 n = 54) comprising several recently diverged forms with unclear taxonomic status are especially interesting. To resolve the taxonomic status of Microtus mystacinus and Microtus kermanensis , we crossed both with Microtus rossiaemeridionalis , and M. kermanensis alone with Microtus arvalis “obscurus” and M. transcaspicus and examined the reproductive performance of their F1 hybrids. All interspecies male hybrids were sterile. Female M. kermanensis × M. arvalis and M. kermanensis × M. transcaspicus hybrids were sterile as well. Therefore, M. mystacinus , M. kermanensis , and M. rossiaemeridionalis could be considered valid species. To gain an insight into the cytological mechanisms of male hybrid sterility, we carried out a histological analysis of spermatogenesis and a cytological analysis of chromosome synapsis, recombination, and epigenetic chromatin modifications in the germ cells of the hybrids using immunolocalization of key meiotic proteins. The hybrids showed wide variation in the onset of spermatogenesis arrest stage, from mature (although abnormal) spermatozoa to spermatogonia only. Chromosome asynapsis was apparently the main cause of meiotic arrest. The degree of asynapsis varied widely across cells, individuals, and the crosses—from partial asynapsis of several small bivalents to complete asynapsis of all chromosomes. The asynapsis was accompanied by a delayed repair of DNA double-strand breaks marked by RAD51 antibodies and silencing of unpaired chromatin marked by γH2A.X antibodies. Overall, the severity of disturbances in spermatogenesis in general and in chromosome synapsis in particular increased in the hybrids with an increase in the phylogenetic distance between their parental species.
The paper reports on the study of flow structure of a reacting propane-air jet, issued from contraction nozzle and impinged on flat metallic surface, by using the particle image velocimetry technique. Flows with different nozzle-to-surface distance H/d were studied. The Reynolds number Re was in the range of 500÷5500, equivalence ratio Φ was varied from 0.8 to 1.4. Velocity field was measured for a conical premixed flame for Re = 1500 and Φ = 0.9. A region with flow recirculation was detected between the flame cone and the impingement surface for the case of H/d = 4. This flow feature may result in a reduced local heat transfer.
Experimental studies of photocatalytic oxidation (PCO) of VX-gas simulation substance cysteamine-S-phosphate sodium salt (NaHPO3S–CH2–CH2–NH2, CPSS) at various initial concentrations and pH were undertaken. PCO ultimately resulted in complete mineralisation of CPSS. The PCO byproducts of CPSS include acetate, oxalate and trace amounts of formate ions. The formation rates of acetate and phosphate were equal to the rate of degradation of CPSS, which indicates easy breakage of P–S, C–S and C–N bonds. Sulphate was formed more slowly due to stepwise oxidation of reduced sulphur. Amino group, generally transformed to ammonia, was partially oxidised to nitrite and nitrate in alkaline media. The fastest mineralisation in terms of both TOC degradation and phosphate formation was observed in neutral media. Under neutral media conditions, the PCO rate increased linearly with the CPSS concentration increase. The maximum efficiency by TOC degradation was observed as large as 77 mg per Wh of incident UV flux with quantum efficiency 3.8%.