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  1. Article ; Online: A predictive surrogate model for hemodynamics and structural prediction in abdominal aorta for different physiological conditions.

    Tang, Xuan / Wu, ChaoJie

    Computer methods and programs in biomedicine

    2023  Volume 243, Page(s) 107931

    Abstract: Background and objective: This study investigates the application of a Predictive Surrogate Model (PSM) for the prediction of the fluid and solid variables in the abdominal aorta by integrating Proper Orthogonal Decomposition (POD) and Long Short-Term ... ...

    Abstract Background and objective: This study investigates the application of a Predictive Surrogate Model (PSM) for the prediction of the fluid and solid variables in the abdominal aorta by integrating Proper Orthogonal Decomposition (POD) and Long Short-Term Memory (LSTM) techniques.
    Methods: The Fluid-Structure Interaction (FSI) solver, which serves as the Full-Order Model (FOM), can capture the blood hemodynamics and structural mechanics precisely for a variety of physiological states, namely the rest and exercise conditions.
    Results: Detailed analyses have been conducted on velocity components, pressure, Wall Shear Stress (WSS), and Oscillatory Shear Index (OSI) variables. Firstly, the reconstruction error has been derived based on a specific number of POD bases to assess the Reduced Order Model (ROM). Notably, the reconstruction error for velocity components in the rest condition is one order of magnitude higher than that in the exercise condition, yet both remained below 10%. This error for pressure is even more minimal, being less than 1%.
    Conclusions: The PSM is evaluated against rest and exercise conditions, exhibiting promising results despite the inherent complexities of the physiological conditions. Despite the inherent complexities of phenomena in the aorta, the predictive model demonstrates consistent error magnitudes for velocity components and wall-related indices, while solid variables show slightly higher errors.
    MeSH term(s) Aorta, Abdominal/physiology ; Blood Flow Velocity/physiology ; Hemodynamics/physiology ; Exercise/physiology ; Stress, Mechanical ; Models, Cardiovascular
    Language English
    Publishing date 2023-11-20
    Publishing country Ireland
    Document type Journal Article
    ZDB-ID 632564-6
    ISSN 1872-7565 ; 0169-2607
    ISSN (online) 1872-7565
    ISSN 0169-2607
    DOI 10.1016/j.cmpb.2023.107931
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Evaluation of 6-PPD quinone toxicity on lung of male BALB/c mice by quantitative proteomics.

    He, Wenmiao / Chao, Jie / Gu, Aihua / Wang, Dayong

    The Science of the total environment

    2024  Volume 922, Page(s) 171220

    Abstract: N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine quinone (6-PPDQ), a transformation product of tyre-derived 6-PPD, has been frequently detected in different environments. After 6-PPDQ exposure, we here aimed to examine dynamic lung bioaccumulation, ... ...

    Abstract N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine quinone (6-PPDQ), a transformation product of tyre-derived 6-PPD, has been frequently detected in different environments. After 6-PPDQ exposure, we here aimed to examine dynamic lung bioaccumulation, lung injury, and the underlying molecular basis in male BALB/c mice. After single injection at concentration of 4 mg/kg, 6-PPDQ remained in lung up to day 28, and higher level of 6-PPDQ bioaccumulation in lung was observed after repeated injection. Severe inflammation was observed in lung after both single and repeated 6-PPDQ injection as indicated by changes of inflammatory cytokines (TNF-α, IL-6 and IL-10). Sirius red staining and hydroxyproline content analysis indicated that repeated rather than single 6-PPDQ injection induced fibrosis in lung. Repeated 6-PPDQ injection also severely impaired lung function in mice by influencing chord compliance (Cchord) and enhanced pause (Penh). Proteomes analysis was further carried out to identify molecular targets of 6-PPDQ after repeated injection, which was confirmed by transcriptional expression analysis and immunohistochemistry staining. Alterations in Ripk1, Fadd, Il-6st, and Il-16 expressions were identified to be associated with inflammation induction of lung after repeated 6-PPDQ injection. Alteration in Smad2 expression was identified to be associated with fibrosis formation in lung of 6-PPDQ exposed mice. Therefore, long-term and repeated 6-PPDQ exposure potentially resulted in inflammation and fibrosis in lung by affecting certain molecular signals in mammals. Our results suggested several aspects of lung injury caused by 6-PPDQ and provide the underlying molecular basis. These observations implied the possible risks of long-term 6-PPDQ exposure to human health.
    MeSH term(s) Male ; Mice ; Humans ; Animals ; Lung Injury/chemically induced ; Mice, Inbred BALB C ; Proteomics ; Lung/pathology ; Inflammation/pathology ; Fibrosis ; Quinones ; Mammals
    Chemical Substances Quinones
    Language English
    Publishing date 2024-02-25
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 121506-1
    ISSN 1879-1026 ; 0048-9697
    ISSN (online) 1879-1026
    ISSN 0048-9697
    DOI 10.1016/j.scitotenv.2024.171220
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Potential-resolved electrochemiluminescence for simultaneous determination of multiplex bladder cancer markers.

    Wang, Junke / Guo, Fenglian / Zhang, Jingjing / Chao, Jie

    Chemical communications (Cambridge, England)

    2024  Volume 60, Issue 34, Page(s) 4609–4612

    Abstract: A novel ECL immunosensor was developed for simultaneous determination of multiplex bladder cancer markers. DNA tetrahedra act as capture probes, while Ru-MOF@AuNPs and AuAgNCs act as signal reporters, yielding well-separated signals reflecting NUMA1 and ... ...

    Abstract A novel ECL immunosensor was developed for simultaneous determination of multiplex bladder cancer markers. DNA tetrahedra act as capture probes, while Ru-MOF@AuNPs and AuAgNCs act as signal reporters, yielding well-separated signals reflecting NUMA1 and CFHR1 concentrations. This strategy offers a new platform for clinical immunoassays, enabling simultaneous multiplex tumor marker detection.
    Language English
    Publishing date 2024-04-23
    Publishing country England
    Document type Journal Article
    ZDB-ID 1472881-3
    ISSN 1364-548X ; 1359-7345 ; 0009-241X
    ISSN (online) 1364-548X
    ISSN 1359-7345 ; 0009-241X
    DOI 10.1039/d4cc00996g
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Comparison of intestinal toxicity in enhancing intestinal permeability and in causing ROS production of six PPD quinones in Caenorhabditis elegans.

    Wang, Yuxing / Liang, Geyu / Chao, Jie / Wang, Dayong

    The Science of the total environment

    2024  Volume 927, Page(s) 172306

    Abstract: As the derivatives of p-phenylenediamines (PPDs), PPD quinones (PPDQs) have received increasing attention due to their possible exposure risk. We compared the intestinal toxicity of six PPDQs (6-PPDQ, 77PDQ, CPPDQ, DPPDQ, DTPDQ and IPPDQ) in ... ...

    Abstract As the derivatives of p-phenylenediamines (PPDs), PPD quinones (PPDQs) have received increasing attention due to their possible exposure risk. We compared the intestinal toxicity of six PPDQs (6-PPDQ, 77PDQ, CPPDQ, DPPDQ, DTPDQ and IPPDQ) in Caenorhabditis elegans. In the range of 0.01-10 μg/L, only 77PDQ (10 μg/L) moderately induced the lethality. All the examined PPDQs at 0.01-10 μg/L did not affect intestinal morphology. Different from this, exposure to 6-PPDQ (1-10 μg/L), 77PDQ (0.1-10 μg/L), CPPDQ (1-10 μg/L), DPPDQ (1-10 μg/L), DTPDQ (1-10 μg/L), and IPPDQ (10 μg/L) enhanced intestinal permeability to different degrees. Meanwhile, exposure to 6-PPDQ (0.1-10 μg/L), 77PDQ (0.01-10 μg/L), CPPDQ (0.1-10 μg/L), DPPDQ (0.1-10 μg/L), DTPDQ (1-10 μg/L), and IPPDQ (1-10 μg/L) resulted in intestinal reactive oxygen species (ROS) production and activation of both SOD-3::GFP and GST-4::GFP. In 6-PPDQ, 77PDQ, CPPDQ, DPPDQ, DTPDQ, and/or IPPDQ exposed nematodes, the ROS production was strengthened by RNAi of genes (acs-22, erm-1, hmp-2, and pkc-3) governing functional state of intestinal barrier. Additionally, expressions of acs-22, erm-1, hmp-2, and pkc-3 were negatively correlated with intestinal ROS production in nematodes exposed to 6-PPDQ, 77PDQ, CPPDQ, DPPDQ, DTPDQ, and/or IPPDQ. Therefore, exposure to different PPDQs differentially induced the intestinal toxicity on nematodes. Our data highlighted potential exposure risk of PPDQs at low concentrations to organisms by inducing intestinal toxicity.
    MeSH term(s) Animals ; Caenorhabditis elegans/drug effects ; Caenorhabditis elegans/physiology ; Reactive Oxygen Species/metabolism ; Quinones/toxicity ; Permeability ; Phenylenediamines/toxicity ; Intestines/drug effects ; Intestines/physiology ; Intestinal Mucosa/metabolism ; Intestinal Barrier Function
    Chemical Substances Reactive Oxygen Species ; Quinones ; Phenylenediamines
    Language English
    Publishing date 2024-04-07
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 121506-1
    ISSN 1879-1026 ; 0048-9697
    ISSN (online) 1879-1026
    ISSN 0048-9697
    DOI 10.1016/j.scitotenv.2024.172306
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: DNA Origami-Enabled Gene Localization of Repetitive Sequences.

    Xiong, Jinxin / He, Zhimei / Wang, Lianhui / Fan, Chunhai / Chao, Jie

    Journal of the American Chemical Society

    2024  Volume 146, Issue 9, Page(s) 6317–6325

    Abstract: Repetitive sequences, which make up over 50% of human DNA, have diverse applications in disease diagnosis, forensic identification, paternity testing, and population genetic analysis due to their crucial functions for gene regulation. However, ... ...

    Abstract Repetitive sequences, which make up over 50% of human DNA, have diverse applications in disease diagnosis, forensic identification, paternity testing, and population genetic analysis due to their crucial functions for gene regulation. However, representative detection technologies such as sequencing and fluorescence imaging suffer from time-consuming protocols, high cost, and inaccuracy of the position and order of repetitive sequences. Here, we develop a precise and cost-effective strategy that combines the high resolution of atomic force microscopy with the shape customizability of DNA origami for repetitive sequence-specific gene localization. "Tri-block" DNA structures were specifically designed to connect repetitive sequences to DNA origami tags, thereby revealing precise genetic information in terms of position and sequence for high-resolution and high-precision visualization of repetitive sequences. More importantly, we achieved the results of simultaneous detection of different DNA repetitive sequences on the gene template with a resolution of ∼6.5 nm (19 nt). This strategy is characterized by high efficiency, high precision, low operational complexity, and low labor/time costs, providing a powerful complement to sequencing technologies for gene localization of repetitive sequences.
    MeSH term(s) Humans ; DNA/genetics ; DNA/chemistry ; Repetitive Sequences, Nucleic Acid ; Chromosome Mapping ; Microscopy, Atomic Force/methods ; Nucleic Acid Conformation ; Nanotechnology/methods
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2024-02-23
    Publishing country United States
    Document type Journal Article
    ZDB-ID 3155-0
    ISSN 1520-5126 ; 0002-7863
    ISSN (online) 1520-5126
    ISSN 0002-7863
    DOI 10.1021/jacs.4c00039
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  6. Article ; Online: Self-assembly of DNA origami for nanofabrication, biosensing, drug delivery, and computational storage.

    He, Zhimei / Shi, Kejun / Li, Jinggang / Chao, Jie

    iScience

    2023  Volume 26, Issue 5, Page(s) 106638

    Abstract: Since the pioneering work of immobile DNA Holliday junction by Ned Seeman in the early 1980s, the past few decades have witnessed the development of DNA nanotechnology. In particular, DNA origami has pushed the field of DNA nanotechnology to a new level. ...

    Abstract Since the pioneering work of immobile DNA Holliday junction by Ned Seeman in the early 1980s, the past few decades have witnessed the development of DNA nanotechnology. In particular, DNA origami has pushed the field of DNA nanotechnology to a new level. It obeys the strict Watson-Crick base pairing principle to create intricate structures with nanoscale accuracy, which greatly enriches the complexity, dimension, and functionality of DNA nanostructures. Benefiting from its high programmability and addressability, DNA origami has emerged as versatile nanomachines for transportation, sensing, and computing. This review will briefly summarize the recent progress of DNA origami, two-dimensional pattern, and three-dimensional assembly based on DNA origami, followed by introduction of its application in nanofabrication, biosensing, drug delivery, and computational storage. The prospects and challenges of assembly and application of DNA origami are also discussed.
    Language English
    Publishing date 2023-04-10
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 2589-0042
    ISSN (online) 2589-0042
    DOI 10.1016/j.isci.2023.106638
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  7. Article ; Online: Single-Molecule Nanomechanical Genotyping with DNA Origami-Based Shape IDs.

    Li, Qian / Chao, Jie / Zhang, Honglu / Fan, Chunhai

    Methods in molecular biology (Clifton, N.J.)

    2023  Volume 2639, Page(s) 147–156

    Abstract: Atomic force microscopy (AFM)-based nanomechanical imaging provides a sub-10-nm-resolution approach for imaging biomolecules under ambient conditions. Here we describe how to generate a set of DNA origami-based shape IDs (triangular and cross shape, with ...

    Abstract Atomic force microscopy (AFM)-based nanomechanical imaging provides a sub-10-nm-resolution approach for imaging biomolecules under ambient conditions. Here we describe how to generate a set of DNA origami-based shape IDs (triangular and cross shape, with and without streptavidin) to site-specifically label target genomic DNA sequences containing two single-nucleotide polymorphisms (SNPs). Adjacent labeling sites separated by only 30 nucleobases (~10 nm) can be differentiated under AFM imaging. We can directly genotype single molecules of human genomic DNA.
    MeSH term(s) Humans ; Genotype ; Nucleic Acid Conformation ; DNA/genetics ; Nanotechnology/methods ; Microscopy, Atomic Force/methods ; Nanostructures
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2023-05-11
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-3028-0_9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Recent Advances in DNA Nanotechnology-Enabled Biosensors for Virus Detection.

    Yuwen, Lihui / Zhang, Shifeng / Chao, Jie

    Biosensors

    2023  Volume 13, Issue 8

    Abstract: Virus-related infectious diseases are serious threats to humans, which makes virus detection of great importance. Traditional virus-detection methods usually suffer from low sensitivity and specificity, are time-consuming, have a high cost, etc. Recently, ...

    Abstract Virus-related infectious diseases are serious threats to humans, which makes virus detection of great importance. Traditional virus-detection methods usually suffer from low sensitivity and specificity, are time-consuming, have a high cost, etc. Recently, DNA biosensors based on DNA nanotechnology have shown great potential in virus detection. DNA nanotechnology, specifically DNA tiles and DNA aptamers, has achieved atomic precision in nanostructure construction. Exploiting the programmable nature of DNA nanostructures, researchers have developed DNA nanobiosensors that outperform traditional virus-detection methods. This paper reviews the history of DNA tiles and DNA aptamers, and it briefly describes the Baltimore classification of virology. Moreover, the advance of virus detection by using DNA nanobiosensors is discussed in detail and compared with traditional virus-detection methods. Finally, challenges faced by DNA nanobiosensors in virus detection are summarized, and a perspective on the future development of DNA nanobiosensors in virus detection is also provided.
    MeSH term(s) Humans ; Aptamers, Nucleotide ; Nanotechnology ; Nanostructures ; DNA
    Chemical Substances Aptamers, Nucleotide ; DNA (9007-49-2)
    Language English
    Publishing date 2023-08-15
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2662125-3
    ISSN 2079-6374 ; 2079-6374
    ISSN (online) 2079-6374
    ISSN 2079-6374
    DOI 10.3390/bios13080822
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  9. Article ; Online: Programmable Nanostructures Based on Framework-DNA for Applications in Biosensing.

    Liu, Bing / Wang, Fan / Chao, Jie

    Sensors (Basel, Switzerland)

    2023  Volume 23, Issue 6

    Abstract: DNA has been actively utilized as bricks to construct exquisite nanostructures due to their unparalleled programmability. Particularly, nanostructures based on framework DNA (F-DNA) with controllable size, tailorable functionality, and precise ... ...

    Abstract DNA has been actively utilized as bricks to construct exquisite nanostructures due to their unparalleled programmability. Particularly, nanostructures based on framework DNA (F-DNA) with controllable size, tailorable functionality, and precise addressability hold excellent promise for molecular biology studies and versatile tools for biosensor applications. In this review, we provide an overview of the current development of F-DNA-enabled biosensors. Firstly, we summarize the design and working principle of F-DNA-based nanodevices. Then, recent advances in their use in different kinds of target sensing with effectiveness have been exhibited. Finally, we envision potential perspectives on the future opportunities and challenges of biosensing platforms.
    MeSH term(s) DNA/chemistry ; Nanostructures/chemistry ; Biosensing Techniques
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2023-03-21
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2052857-7
    ISSN 1424-8220 ; 1424-8220
    ISSN (online) 1424-8220
    ISSN 1424-8220
    DOI 10.3390/s23063313
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  10. Article ; Online: DNA-Based Gold Nanoparticle Assemblies: From Structure Constructions to Sensing Applications.

    Xie, Mo / Jiang, Jinke / Chao, Jie

    Sensors (Basel, Switzerland)

    2023  Volume 23, Issue 22

    Abstract: Gold nanoparticles (Au NPs) have become one of the building blocks for superior assembly and device fabrication due to the intrinsic, tunable physical properties of nanoparticles. With the development of DNA nanotechnology, gold nanoparticles are ... ...

    Abstract Gold nanoparticles (Au NPs) have become one of the building blocks for superior assembly and device fabrication due to the intrinsic, tunable physical properties of nanoparticles. With the development of DNA nanotechnology, gold nanoparticles are organized in a highly precise and controllable way under the mediation of DNA, achieving programmability and specificity unmatched by other ligands. The successful construction of abundant gold nanoparticle assembly structures has also given rise to the fabrication of a wide range of sensors, which has greatly contributed to the development of the sensing field. In this review, we focus on the progress in the DNA-mediated assembly of Au NPs and their application in sensing in the past five years. Firstly, we highlight the strategies used for the orderly organization of Au NPs with DNA. Then, we describe the DNA-based assembly of Au NPs for sensing applications and representative research therein. Finally, we summarize the advantages of DNA nanotechnology in assembling complex Au NPs and outline the challenges and limitations in constructing complex gold nanoparticle assembly structures with tailored functionalities.
    MeSH term(s) Gold/chemistry ; Metal Nanoparticles/chemistry ; DNA/chemistry ; Nanotechnology
    Chemical Substances Gold (7440-57-5) ; DNA (9007-49-2)
    Language English
    Publishing date 2023-11-16
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2052857-7
    ISSN 1424-8220 ; 1424-8220
    ISSN (online) 1424-8220
    ISSN 1424-8220
    DOI 10.3390/s23229229
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