56 research outputs found

    In situ Chromatin Interaction Analysis Using Paired-End Tag Sequencing.

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    Chromatin Interaction Analysis Using Paired-End Tag Sequencing (ChIA-PET) is an established method to map protein-mediated chromatin interactions. A limitation, however, is that it requires a hundred million cells per experiment, which hampers its broad application in biomedical research, particularly in studies in which it is impractical to obtain a large number of cells from rare samples. To reduce the required input cell number while retaining high data quality, we developed an in situ ChIA-PET protocol, which requires as few as 1 million cells. Here, we describe detailed step-by-step procedures for performing in situ ChIA-PET from cultured cells, including both an experimental protocol for sample preparation and data generation and a computational protocol for data processing and visualization using the ChIA-PIPE pipeline. As the protocol significantly simplifies the experimental procedure, reduces ligation noise, and decreases the required input of cells compared to previous versions of ChIA-PET protocols, it can be applied to generate high-resolution chromatin contact maps mediated by various protein factors for a wide range of human and mouse primary cells. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Sample preparation and data generation Support Protocol: Bridge linker preparation Basic Protocol 2: Data processing and visualization

    First detection of Cryptosporidium spp. in red-bellied tree squirrels (Callosciurus erythraeus) in China

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    Cryptosporidium spp. are opportunistic pathogens that cause diarrhea in a variety of animal hosts. Although they have been reported in many animals, no information has been published on the occurrence of Cryptosporidium spp. in red-bellied tree squirrels (Callosciurus erythraeus). A total of 287 fecal specimens were collected from Sichuan province in China; the prevalence of Cryptosporidium spp., measured by nested-PCR amplification of the partial small-subunit (SSU) rRNA gene, was 1.4% (4/287). Three different Cryptosporidium species or genotypes were identified: Cryptosporidium parvum (n = 1), Cryptosporidium wrairi (n = 1), and Cryptosporidium rat genotype II (n = 2). The present study is the first report of Cryptosporidium infection in red-bellied tree squirrels in China. Although there is a relatively low occurrence of Cryptosporidium, the presence of C. parvum and C. wrairi, which were previously reported in humans, indicates that red-bellied tree squirrels may be a source of zoonotic cryptosporidiosis in China

    Study on Stress Development in the Phase Transition Layer of Thermal Barrier Coatings

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    Stress development is one of the significant factors leading to the failure of thermal barrier coating (TBC) systems. In this work, stress development in the two phase mixed zone named phase transition layer (PTL), which grows between the thermally grown oxide (TGO) and the bond coat (BC), is investigated by using two different homogenization models. A constitutive equation of the PTL based on the Reuss model is proposed to study the stresses in the PTL. The stresses computed with the proposed constitutive equation are compared with those obtained with Voigt model-based equation in detail. The stresses based on the Voigt model are slightly higher than those based on the Reuss model. Finally, a further study is carried out to explore the influence of phase transition proportions on the stress difference caused by homogenization models. Results show that the stress difference becomes more evident with the increase of the PTL thickness ratio in the TGO

    Oxidation Simulation of Thermal Barrier Coatings with Actual Microstructures Considering Strength Difference Property and Creep-Plastic Behavior

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    A scanning electron microscope (SEM) image based direct finite element (FE) mesh reconstruction method is employed to reflect microstructure features of thermal barrier coatings (TBC). The creep-plastic assumption of thermally grown oxide (TGO) scale and metallic bond coat (BC) as well as the strength difference (SD) property of ceramic top coat (TC) are considered to simulate the mechanical behavior. A diffusion oxidation model considering oxygen consumption is proposed to characterize TGO growth. The oxidation simulation of TBC is carried out under the consideration of actual microstructure features. The results revealed that the interface defects increase the surface-area-to-volume ratio of BC exposed to oxygen anion. This leads to the non-uniform TGO growth, which has also been observed in experimental studies. The microstructures and mechanical behavior strongly affect stress evolution in TBC. The consideration of actual microstructure features and reasonable mechanical behaviors, including the creep-plastic behavior and SD property, is helpful for the accurate evaluation of interface stress

    Study on Stress Development in the Phase Transition Layer of Thermal Barrier Coatings

    No full text
    Stress development is one of the significant factors leading to the failure of thermal barrier coating (TBC) systems. In this work, stress development in the two phase mixed zone named phase transition layer (PTL), which grows between the thermally grown oxide (TGO) and the bond coat (BC), is investigated by using two different homogenization models. A constitutive equation of the PTL based on the Reuss model is proposed to study the stresses in the PTL. The stresses computed with the proposed constitutive equation are compared with those obtained with Voigt model-based equation in detail. The stresses based on the Voigt model are slightly higher than those based on the Reuss model. Finally, a further study is carried out to explore the influence of phase transition proportions on the stress difference caused by homogenization models. Results show that the stress difference becomes more evident with the increase of the PTL thickness ratio in the TGO

    Interaction Forces between Diaspore and Kaolinite in NaOL Solution Probed by EDLVO Theory and AFM Analysis

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    Molecular force plays an important role in the interaction between collector and minerals, which directly reflects the intrinsic reason for the selectivity and collection of the collector to minerals. In this work, the interaction forces between sodium oleate (NaOL) and minerals (kaolinite and diaspore) were directly characterized by atomic force microscopy (AFM) combined with EDLVO theory. The results show that after interacting with NaOL, the zeta potentials of kaolinite and diaspore were more negative, and the hydrophobicity of minerals increased. EDLVO calculation results indicate that electrostatic repulsion dominated the interaction forces between mineral particles, and the van der Waals interaction energy, electrostatic interaction energy, and hydrophobic interaction energy increased after NaOL treatment. AFM measurements show that the NaOL collector increased the attraction force of diaspore-diaspore and kaolinite-kaolinite particles, and the increase in attraction force for diaspore-diaspore particles was larger than in kaolinite particles, which was consistent with the EDLVO results. The adhesion force between the NaOL collector and the diaspore surface was larger than in kaolinite, confirming the fact that NaOL had better collection and selectivity for diaspore than kaolinite. This work improves understanding of the interaction mechanisms between NaOL collector, diaspore, and kaolinite minerals

    Interaction Forces between Diaspore and Kaolinite in NaOL Solution Probed by EDLVO Theory and AFM Analysis

    No full text
    Molecular force plays an important role in the interaction between collector and minerals, which directly reflects the intrinsic reason for the selectivity and collection of the collector to minerals. In this work, the interaction forces between sodium oleate (NaOL) and minerals (kaolinite and diaspore) were directly characterized by atomic force microscopy (AFM) combined with EDLVO theory. The results show that after interacting with NaOL, the zeta potentials of kaolinite and diaspore were more negative, and the hydrophobicity of minerals increased. EDLVO calculation results indicate that electrostatic repulsion dominated the interaction forces between mineral particles, and the van der Waals interaction energy, electrostatic interaction energy, and hydrophobic interaction energy increased after NaOL treatment. AFM measurements show that the NaOL collector increased the attraction force of diaspore-diaspore and kaolinite-kaolinite particles, and the increase in attraction force for diaspore-diaspore particles was larger than in kaolinite particles, which was consistent with the EDLVO results. The adhesion force between the NaOL collector and the diaspore surface was larger than in kaolinite, confirming the fact that NaOL had better collection and selectivity for diaspore than kaolinite. This work improves understanding of the interaction mechanisms between NaOL collector, diaspore, and kaolinite minerals

    Asymmetric full mode-converting transmission of elastic waves

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    Asymmetric transmission in which wave energy propagates only in one direction attracts significant attention in various fields because of its rich physics and potential applications. In this work, we propose an elastic mode-converting metamaterial, which allows a full-power mode-converting transmission from longitudinal waves to transverse waves in the forward direction, while completely restricts the L wave transmission in the inverse direction. The metamaterial is designed by simply cutting two arrays of periodic silts on a matrix by exploring a straight design methodology, and thus very friendly for fabrication and application. Eigen-frequency analysis shows that the bilayer metamaterial exhibits two modes with significantly close natural frequencies around the working frequency, one for full-power mode-converting transmission, and the other for asymmetric transmission. Ultrasonic experiments are carried out to validate the proposed design. Our work offers a simple and efficient way for the realization of a complete one-way mode-converting transmission, and could be critically useful in designing diode-like meta-devices for novel wave manipulations
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