Hengzongshu/ArticleAgent huggingface dataset:
Reproductive potential is the most important conditional indicator reflecting the ability of individuals in a population to reproduce, survive and develop under optimal environmental conditions. As for humans, the concept of reproductive potential can include the level of the individual’s mental and physical state, which allows them to reproduce healthy offspring when they reach social and physical maturity. Female reproductive potential has been investigated in great detail, whereas the male reproductive potential (MRP) has not received the equal amount of attention as yet. Therefore, here we focused on the human Y chromosome and found candidate single-nucleotide polymorphism (SNP) markers of MRP. With our development named Web-service SNP_TATA_Z-tester, we examined in silico all 35 unannotated SNPs within 70-bp proximal promoters of the three Y-linked genes, CDY2A, SHOX and ZFY, which represent all types of human Y-chromosome genes, namely: unique, pseudo-autosomal, and human X-chromosome gene paralogs, respectively. As a result, we found 11 candidate SNP markers for MRP, which can significantly alter the TATA-binding protein (TBP) binding affinity for promoters of these genes. First of all, we selectively verified in vitro the values of the TBP-promoter affinity under this study, Pearson’s linear correlation between predicted and measured values of which were r = 0.94 (significance p < 0.005). Next, as a discussion, using keyword search tools of the PubMed database, we found clinically proven physiological markers of human pathologies, which correspond to a change in the expression of the genes carrying the candidate SNP markers predicted here. These were markers for spermatogenesis disorders (ZFY: rs1388535808 and rs996955491), for male maturation arrest (CDY2A: rs200670724) as well as for disproportionate short stature at Madelung deformity (e. g., SHOX: rs1452787381) and even for embryogenesis disorders (e. g., SHOX: rs28378830). This indicates a wide range of MRI indicators, alterations in which should be expected in the case of SNPs in the promoters of the human Y-chromosome genes and which can go far beyond changes in male fertility.
Genetic diversity between of the Novosibirsk and Tomsk chromosome races of the common shrew (Sorex araneus) was analyzed

using 39 polymorphic AFLP (amplified fragments length polymorphism) markers. Exact and F-statistics tests for population differentiation demonstrated significant interracial difference in allele frequencies and significant subdivision between the races

The value of the genetic distance between the chromosome races observed in this study corresponds to that found between subspecies of mammals studied so far
Experimental hybridization of X0 and XY chromosome races of the brachypterous grasshopper P. sapporensis did not reveal pre-zygotic reproductive isolation.However, a partial zygotic barrier was found between the X0-standard race from Shimokawa and XY-standard chromosome race from Akan.Approximately 40% of embryos from females crossed with males from other chromosome races developed parthenogenetically, the remaining embryos were normal heterozygotes.Adult F1 males and females from crosses of this type had properly developed testes and ovaries.Non-sister associations and other irregularities in meiosis were not observed in male meiosis.Crossing experiments demonstrated that hybrids between X0 and XY races occur to some extent.The absence of a hybrid zone between the X0 and XY chromosome races may be the result of selection against heterozygotes.Crosses between the XY-Tanno and X0-standard (Teine) subraces resulted in F1 and F2 generations in spite of the many chromosome differences between them such as a X-A translocation and fixed pericentric inversions in four pairs of autosomes.These results do not support the hypothesis that chromosomal differences play a key role in restricting gene flow between the X0 and XY races of P. sapporensis.
We report a search for the decays $B^0\to K^{*0} \overline{K}{}^{*0}$ and $B^0\to K^{*0} K^{*0}$. We also measure other charmless decay modes with $K^+\pi^-K^-\pi^+$ and $K^{+}\pi^{-}K^{+}\pi^{-}$ final states. The results are obtained from a data sample containing $657 \times 10^6$ $B \overline B$ pairs collected with the Belle detector at the KEKB asymmetric-energy $e^+e^-$ collider. We set upper limits on the branching fractions for $B^0\to K^{*0} \kstarbar$ and $B^0\to K^{*0} K^{*0}$ of $0.81 \times 10^{-6}$ and $0.20\times 10^{-6}$, respectively, at the 90% confidence level.
To reveal the molecular mechanism of anti-angiogenic activity of semisynthetic triterpenoid CDDO-Im.Using re-analysis of cDNA microarray data of CDDO-Im-treated human vascular endothelial cells (HUVECs) (GSE71622), functional annotation of revealed differentially expressed genes (DEGs) and analysis of their co-expression, the key processes induced by CDDO-Im in HUVECs were identified. Venn diagram analysis was further performed to reveal the common DEGs, i.e. genes both susceptible to CDDO-Im and involved in the regulation of angiogenesis. A list of probable protein targets of CDDO-Im was prepared based on Connectivity Map/cheminformatics analysis and chemical proteomics data, among which the proteins that were most associated with the angiogenesis-related regulome were identified. Finally, identified targets were validated by molecular docking and text mining approaches.The effect of CDDO-Im in HUVECs can be divided into two main phases: the short early phase (0.5-3 h) with an acute FOXD1/CEBPA/JUNB-regulated pro-angiogenic response induced by xenobiotic stress, and the second anti-angiogenic step (6-24 h) with massive suppression of various angiogenesis-related processes, accompanied by the activation of cytoprotective mechanisms. Our analysis showed that the anti-angiogenic activity of CDDO-Im is mediated by its inhibition of the expression of PLAT, ETS1, A2M, SPAG9, RASGRP3, FBXO32, GCNT1 and HDGFRP3 and its direct interactions with EGFR, mTOR, NOS2, HSP90AA1, MDM2, SYK, IRF3, ATR and KIF14.Our findings provide valuable insights into the understanding of the molecular mechanisms of the anti-angiogenic activity of cyano enone-bearing triterpenoids and revealed a range of novel promising therapeutic targets to control pathological neovascularization.
Simulations of first-passage folding of the antiparallel β-sheet miniprotein beta3s, which has been intensively studied under equilibrium conditions by A. Caflisch and co-workers, show that the kinetics and dynamics are significantly different from those for equilibrium folding. Because the folding of a protein in a living system generally corresponds to the former (i.e., the folded protein is stable and unfolding is a rare event), the difference is of interest.

In contrast to equilibrium folding, the Ch-curl conformations become very rare because they contain unfavorable parallel β-strand arrangements, which are difficult to form dynamically due to the distant N- and C-terminal strands. At the same time, the formation of helical conformations becomes much easier (particularly in the early stage of folding) due to short-range contacts. The hydrodynamic descriptions of the folding reaction have also revealed that while the equilibrium flow field presented a collection of local vortices with closed "streamlines", the first-passage folding is characterized by a pronounced overall flow from the unfolded states to the native state. The flows through the locally stable structures Cs-or and Ns-or, which are conformationally close to the native state, are negligible due to detailed balance established between these structures and the native state.

Although there are significant differences in the general picture of the folding process from the equilibrium and first-passage folding simulations, some aspects of the two are in agreement. The rate of transitions between the clusters of characteristic protein conformations in both cases decreases approximately exponentially with the distance between the clusters in the hydrogen bond distance space of collective variables, and the folding time distribution in the first-passage segments of the equilibrium trajectory is in good agreement with that for the first-passage folding simulations.
The Eurasian malaria vector Anopheles messeae is a widely spread and genetically diverse species. Five widespread polymorphic chromosomal inversions were found in natural populations of this mosquito. A cryptic species, Anopheles daciae, was differentiated from An. messeae by the presence of several nucleotide substitutions in the Internal Transcribed Spacer 2 (ITS2) region of ribosomal DNA. However, because of the absence of a high-quality reference cytogenetic map, the inversion polymorphisms in An. daciae and An. messeae remain poorly understood. Moreover, a recently determined heterogeneity in ITS2 in An. daciae questioned the accuracy of the previously used Restriction Fragment Length Polymorphism (RFLP) assay for species diagnostics.

In this study, a standard-universal cytogenetic map was constructed based on orcein stained images of chromosomes from salivary glands for population studies of the chromosomal inversions that can be used for both An. messeae and An. daciae. In addition, a new ITS2-RFLP approach for species diagnostics was developed. Both methods were applied to characterize inversion polymorphism in populations of An. messeae and An. daciae from a single location in Western Siberia in Russia.

The analysis demonstrates that cryptic species are remarkably different in their frequencies of chromosomal inversion variants. Our study supports previous observations that An. messeae has higher inversion polymorphism in all autosomes than the cryptic species An. daciae.
At extreme pressures and temperatures common materials form new dense phases with compacted atomic arrangements. By classical molecular dynamics simulation we observe that FCC copper undergo phase transformation to BCC structure. The transition occurs under shock wave loading at the pressures above 80 GPa and corresponding temperatures above 2000 K. We calculate phase diagram, show that at these pressures and low temperature FCC phase of copper is still stable and discuss the thermodynamic reason for phase transformation at high temperature shock wave regime. Titanium forms new hexagonal phase at high pressure as well. We calculate the structure of shock wave in titanium and observe that shock front splits in three parts: elastic, plastic and phase transformation. The possibility of using a phase transition behind a shock wave with further unloading for designing nanocrystalline materials with a reduced grain size is also shown.
Combustion of liquid hydrocarbon fuel dispersed by superheated steam jet was experimentally studied.

Characteristics of the combustion process (heat release, emission of toxic products, flame temperature) were investigated in a laboratory direct-flow atmospheric burner (capacity up to 20 kW) at different operating systems with waste transmission automotive oil as fuel example.

Regimes were found which provoke stable combustion of non-quality liquid hydrocarbons. It was shown dependences of heat, flue gas parameters on superheated steam flow rates, fuel flow rates, flame temperatures.
The article is devoted to development of methods of search of information on the Internet. Currently the issue of fast and automatic data extraction from different sources is very actual. The aim of this work is creation of instrument to solve this problem. The idea of the approach is to develop semi-automatic methods of linguistic templates construction for given fragment of atomic diagram. Algorithm of templates construction for the fragment of atomic diagram is performed in 2 stages. On the 1st stage generation of the simple templates is done, on the 2nd stage more seldom and complicated templates are found, using templates from 1st part of algorithm. Processing texts in natural language on the Internet using gotten templates, needed information may be found.
The paper study are the conditions of formation of metal-ceramic tracks regarding the parameters of the laser action.

Optimization of laser action on the powder mixture was carried out. The mechanical properties of laser tracks have been studied.

It is demonstrated that both the ceramic particle size and concentration vary at different focusing modes. It is found that the clad metal-ceramic structure has 4 – 5 times higher microhardness – 854 HV0.1 as compared to the substrate 178 HV0.1.
The discovery of the position effect variegation phenomenon and the subsequent comprehensive analysis of its molecular mechanisms led to understanding that the local chromatin composition has a dramatic effect on gene activity. To study this effect in a high-throughput mode and at the genome-wide level, the Thousands of Reporters Integrated in Parallel (TRIP) approach based on the usage of barcoded reporter gene constructs was recently developed.

Here we describe the construction and quality checks of high-diversity barcoded plasmid libraries supposed to be used for high-throughput analysis of chromatin position effects in Drosophila cells. First, we highlight the critical parameters that should be considered in the generation of barcoded plasmid libraries and introduce a simple method to assess the diversity of random sequences (barcodes) of synthetic oligonucleotides using PCR amplification followed by Sanger sequencing. Second, we compare the conventional restriction-ligation method with the Gibson assembly approach for cloning barcodes into the same plasmid vector. Third, we provide optimized parameters for the construction of barcoded plasmid libraries, such as the vector : insert ratio in the Gibson assembly reaction and the voltage used for electroporation of bacterial cells with ligation products. We also compare different approaches to check the quality of barcoded plasmid libraries. Finally, we briefly describe alternative approaches that can be used for the generation of such libraries.

Importantly, all improvements and modifications of the techniques described here can be applied to a wide range of experiments involving barcoded plasmid libraries.
Within the framework of the skeleton model of a porous medium

numerical simulation of two tasks was performed: task of the absorption of acoustic disturbances at hypersonic flow past a plate with a porous insert taking into account the real properties of the gas and task of a supersonic flow around a streamwise aligned cylinder with a frontal insert from cellular porous nickel

It is shown that high porous cellular materials can effectively be used in supersonic aerodynamics
Within a plane-wave approximation in scattering, an incoming wave packet's Wigner function stays positive everywhere, which obscures such purely quantum phenomena as nonlocality and entanglement. With the advent of the electron microscopes with subnanometer-sized beams, one can enter a genuinely quantum regime where the latter effects become only moderately attenuated. Here we show how to probe negative values of the Wigner function in scattering of a coherent superposition of two Gaussian packets with a nonvanishing impact parameter between them (a Schr\"odinger's cat state) by atomic targets. For hydrogen in the ground $1s$ state, a small parameter of the problem, a ratio $a/{\ensuremath{\sigma}}_{\ensuremath{\perp}}$ of the Bohr radius $a$ to the beam width ${\ensuremath{\sigma}}_{\ensuremath{\perp}}$, is no longer vanishing. We predict an azimuthal asymmetry of the scattered electrons, which is found to be up to 10%, and argue that it can be reliably detected. The production of beams with the not-everywhere-positive Wigner functions and the probing of such quantum effects can open new perspectives for noninvasive electron microscopy, quantum tomography, particle physics, and so forth.
The article discusses legislative changes regarding new public easements, in particular public easements in relation to public lands and public easements for certain purposes. Their differences from public easements that existed earlier in accordance with the classical theory of limited property rights are discussed.

The jurisprudence is analyzed in the framework of attracting forensic experts in cases of establishing public easements.

Cases of attracting experts in litigation for land surveying are identified.
Retrotransposons comprise a ubiquitous and abundant class of eukaryotic transposable elements. All members of this class rely on reverse transcriptase activity to produce a DNA copy of the element from the RNA template. However, other activities of the retrotransposon-encoded polyprotein may differ between diverse retrotransposons. The polyprotein domains corresponding to each of these activities may have their own evolutionary history independent from that of the reverse transcriptase, thus underlying the modular view on the evolution of retrotransposons. Furthermore, some transposable elements can independently evolve similar domain architectures by acquiring functionally similar but phylogenetically distinct modules. This convergent evolution of retrotransposons may ultimately suggest similar regulatory pathways underlying the lifecycle of the elements.

Here, we provide new examples of the convergent evolution of retrotransposons of species from two unrelated taxa: green plants and parasitic protozoan oomycetes. In the present study we first analyzed the available genomic sequences of oomycete species and characterized two groups of Ty3/Gypsy long terminal repeat retrotransposons, namely Chronos and Archon, and a subgroup of L1 non-long terminal repeat retrotransposons. The results demonstrated that the retroelements from these three groups each have independently acquired plant-related ribonuclease H domains. This process closely resembles the evolution of retrotransposons in the genomes of green plants. In addition, we showed that Chronos elements captured a chromodomain, mimicking the process of chromodomain acquisition by Chromoviruses, another group of Ty3/Gypsy retrotransposons of plants, fungi, and vertebrates.

Repeated and strikingly similar acquisitions of ribonuclease H domains and chromodomains by different retrotransposon groups from unrelated taxa indicate similar selection pressure acting on these elements. Thus, there are some major trends in the evolution of the structural composition of retrotransposons, and characterizing these trends may enhance the current understanding of the retrotransposon life cycle.
Thermophysical fundamentals and engineering concepts of the two-phase microfluidic devises based on controlled liquid decay are discussed in this paper.

The results of an experimental study of the explosive evaporation at a thin film heater of the MEMS devise in application to thermal inkjet printing are presented. The peculiarities of homogeneous nucleation and bubble growth in the liquid subjected to pulse heating are discussed. Using experimental data a simple equation suitable for predicting the growth rate of a vapor bubble in a non-uniformly superheated liquid was obtained and used to complete a mathematical model of the self-consistent nucleation and vapor bubbles growth in the induced pressure field.

The results of numerical calculations according to the proposed model showed good agreement with the experimental data on a time of nucleation and duration of the initial stage of an explosive evaporation of water.
Parahydrogen-induced polarization (PHIP) is an NMR hyperpolarization technique that increases nuclear spin polarization by orders of magnitude, and it is particularly well-suited to study hydrogenation reactions. However, the use of high-field NMR spectroscopy is not always possible, especially in the context of potential industrial-scale reactor applications. On the other hand, the direct low-field NMR detection of reaction products with enhanced nuclear spin polarization is challenging due to near complete signal cancellation from nascent parahydrogen protons.

We show that hydrogenation products prepared by PHIP can be irradiated with weak (on the order of spin-spin couplings of a few hertz) alternating magnetic field (called Spin-Lock Induced Crossing or SLIC) and consequently efficiently detected at low magnetic field (e.g., 0.05 T used here) using examples of several types of organic molecules containing a vinyl moiety.

The detected hyperpolarized signals from several reaction products at tens of millimolar concentrations were enhanced by 10000-fold, producing NMR signals an order of magnitude greater than the background signal from protonated solvents.
Article Free Access Share on Winnowing sequences from a database search Authors: Piotr Berman Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PAView Profile , Zheng Zhang Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PAView Profile , Yuri I. Wolf National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD and Institute of Cytology and Genetics, Russian Academy of Sciences, Novosibirsk 630090, Russia National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD and Institute of Cytology and Genetics, Russian Academy of Sciences, Novosibirsk 630090, RussiaView Profile , Eugene V. Koonin National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MDView Profile , Webb Miller Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PAView Profile Authors Info & Claims RECOMB '99: Proceedings of the third annual international conference on Computational molecular biologyApril 1999 Pages 50–58https://doi.org/10.1145/299432.299451Online:01 April 1999Publication History 2citation375DownloadsMetricsTotal Citations2Total Downloads375Last 12 Months2Last 6 weeks1 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my Alerts New Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
The article presents a clinical case study of an efficient therapy with infliximab used for a 33-year-old patient with a severe course of psoriasis, psoriatic arthritis, psoriatic onychopathy; chronic hepatitis C with the minimum activity, replication phase; hyper- and normatrophic scars affecting 40% of the body surface; cicatricial contractures; complicated posterior polar cataract of both eyes; secondary amyloidosis of the kidneys with a nephrotic syndrome. It also demonstrates the significance of the anti-cytokine therapy as a method of choice in a complicated clinical situation.
On generic structures preserving elementary equivalence and elementary embeddability

They use classical characterizations for the general case. The criterion for elementary equivalence is based on the well known Fraïssé-Taimanov-Ehrenfeucht overturning method. The criterion for elementary embeddability uses the known Tarski-Vaught test.

We consider criteria for elementary equivalence and elementary embeddability for generic structures.
We review some applications of Gröbner-Shirshov bases, including PBW theorems, linear bases of free universal algebras, normal forms for groups and semigroups, extensions of groups and algebras, embedding of algebras.