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  1. AU="Dong, Yafei"
  2. AU="Ziming Zhang"
  3. AU="Mensah, Derrick"
  4. AU="Albacker, L"
  5. AU="Rupp, Adam"
  6. AU=Chia Helena N
  7. AU="Agostini, Ludovico"
  8. AU="Vieira, Dorice"
  9. AU="Sharma, Arya M"
  10. AU="Lieve E. H. van der Donk"
  11. AU="Großer, Matthias"
  12. AU="Ong, Edison"
  13. AU=Lavery James V
  14. AU=Moss Arthur J
  15. AU="Ni, Dongchun"
  16. AU="Yang, Yanfan"
  17. AU="Shona Manning"
  18. AU=Charters Pia F P AU=Charters Pia F P
  19. AU="Adumuah, Naa N"
  20. AU="Rodrigues, Jonathan Carl Luis"
  21. AU=Seidel Bastian M
  22. AU="Duan Weimin"
  23. AU=Ioanas M
  24. AU="Nancy Zambon"
  25. AU="Kumawat, Sunita"
  26. AU=Bogliacino Francesco
  27. AU="Setter, Peter"
  28. AU=Shikata Chihiro
  29. AU="Jordan P. Metcalf"
  30. AU=Peri?i? Nanut Milica AU=Peri?i? Nanut Milica
  31. AU="Pramod, Ganapathiraju"
  32. AU="Fu, Chu-Jun"
  33. AU="Nejad, Harry G."
  34. AU="Zhang, Q E"
  35. AU="Oppenheim, Madeline"

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  1. Artikel ; Online: Head and Neck Tumor Segmentation from [18F]F-FDG PET/CT Images Based on 3D Diffusion Model.

    Dong, Yafei / Gong, Kuang

    ArXiv

    2024  

    Abstract: Head and neck (H&N) cancers are among the most prevalent types of cancer worldwide, and [18F]F-FDG PET/CT is widely used for H&N cancer management. Recently, the diffusion model has demonstrated remarkable performance in various image-generation tasks. ... ...

    Abstract Head and neck (H&N) cancers are among the most prevalent types of cancer worldwide, and [18F]F-FDG PET/CT is widely used for H&N cancer management. Recently, the diffusion model has demonstrated remarkable performance in various image-generation tasks. In this work, we proposed a 3D diffusion model to accurately perform H&N tumor segmentation from 3D PET and CT volumes. The 3D diffusion model was developed considering the 3D nature of PET and CT images acquired. During the reverse process, the model utilized a 3D UNet structure and took the concatenation of PET, CT, and Gaussian noise volumes as the network input to generate the tumor mask. Experiments based on the HECKTOR challenge dataset were conducted to evaluate the effectiveness of the proposed diffusion model. Several state-of-the-art techniques based on U-Net and Transformer structures were adopted as the reference methods. Benefits of employing both PET and CT as the network input as well as further extending the diffusion model from 2D to 3D were investigated based on various quantitative metrics and the uncertainty maps generated. Results showed that the proposed 3D diffusion model could generate more accurate segmentation results compared with other methods. Compared to the diffusion model in 2D format, the proposed 3D model yielded superior results. Our experiments also highlighted the advantage of utilizing dual-modality PET and CT data over only single-modality data for H&N tumor segmentation.
    Sprache Englisch
    Erscheinungsdatum 2024-01-31
    Erscheinungsland United States
    Dokumenttyp Preprint
    ISSN 2331-8422
    ISSN (online) 2331-8422
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Buch ; Online: Head and Neck Tumor Segmentation from [18F]F-FDG PET/CT Images Based on 3D Diffusion Model

    Dong, Yafei / Gong, Kuang

    2024  

    Abstract: Head and neck (H&N) cancers are among the most prevalent types of cancer worldwide, and [18F]F-FDG PET/CT is widely used for H&N cancer management. Recently, the diffusion model has demonstrated remarkable performance in various image-generation tasks. ... ...

    Abstract Head and neck (H&N) cancers are among the most prevalent types of cancer worldwide, and [18F]F-FDG PET/CT is widely used for H&N cancer management. Recently, the diffusion model has demonstrated remarkable performance in various image-generation tasks. In this work, we proposed a 3D diffusion model to accurately perform H&N tumor segmentation from 3D PET and CT volumes. The 3D diffusion model was developed considering the 3D nature of PET and CT images acquired. During the reverse process, the model utilized a 3D UNet structure and took the concatenation of PET, CT, and Gaussian noise volumes as the network input to generate the tumor mask. Experiments based on the HECKTOR challenge dataset were conducted to evaluate the effectiveness of the proposed diffusion model. Several state-of-the-art techniques based on U-Net and Transformer structures were adopted as the reference methods. Benefits of employing both PET and CT as the network input as well as further extending the diffusion model from 2D to 3D were investigated based on various quantitative metrics and the uncertainty maps generated. Results showed that the proposed 3D diffusion model could generate more accurate segmentation results compared with other methods. Compared to the diffusion model in 2D format, the proposed 3D model yielded superior results. Our experiments also highlighted the advantage of utilizing dual-modality PET and CT data over only single-modality data for H&N tumor segmentation.

    Comment: 28 pages, 5 figures
    Schlagwörter Electrical Engineering and Systems Science - Image and Video Processing ; Computer Science - Computer Vision and Pattern Recognition ; Physics - Medical Physics
    Thema/Rubrik (Code) 004
    Erscheinungsdatum 2024-01-30
    Erscheinungsland us
    Dokumenttyp Buch ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  3. Artikel ; Online: A label free fluorescent aptamer sensor based on the combined action of Graphene oxide and SYBR Green I for the detection of Aflatoxin B1.

    Hu, Mengyang / Cheng, Meng / Wang, Na / Sang, Yidan / Dong, Yafei / Wang, Luhui

    IEEE transactions on nanobioscience

    2024  Band PP

    Abstract: Here, based on the characteristics of Graphene oxide(GO) and SYBR Green I(SGI) dye, an enzyme-free and label-free fluorescent biosensor with signal amplification through DNA strand reaction is proposed for the detection of Aflatoxin B1(AFB1) in food ... ...

    Abstract Here, based on the characteristics of Graphene oxide(GO) and SYBR Green I(SGI) dye, an enzyme-free and label-free fluorescent biosensor with signal amplification through DNA strand reaction is proposed for the detection of Aflatoxin B1(AFB1) in food safety. Firstly, without the addition of AFB1, the substrate in the system includes a double stranded Apt-S with a long sticky end and two hairpins H1 and H2. Although the complementary pairing of bases may exhibit fluorescence due to the insertion of SGI dyes, the use of GO, which is highly capable of adsorbing single stranded parts and quenching fluorescence, cleverly reduces the background fluorescence. Adding the target AFB1 triggers DNA inter chain reactions, generating a large amount of long double stranded DNA H1-H2, thereby generating strong fluorescence signals under the action of SGI. More importantly, logical theory verification and computer simulation were conducted before biological experiments, providing a theoretical basis for the implementation of the biosensor. After analysis, the fluorescence biosensor exhibits a good linear relationship with AFB1 concentration in the range of 5-50nM, with a detection limit of 0.76nM. It also has good specificity, anti-interference ability, and practical application ability, and has broad application prospects in the field of food safety.
    Sprache Englisch
    Erscheinungsdatum 2024-05-20
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ISSN 1558-2639
    ISSN (online) 1558-2639
    DOI 10.1109/TNB.2024.3403158
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel ; Online: Design and Simulation of an Autonomous Molecular Mechanism Using Spatially Localized DNA Computation.

    Wang, Yue / Wang, Luhui / Hu, Wenxiao / Qian, Mengyao / Dong, Yafei

    Interdisciplinary sciences, computational life sciences

    2023  Band 15, Heft 1, Seite(n) 1–14

    Abstract: As a well-established technique, DNA synthesis offers interesting possibilities for designing multifunctional nanodevices. The micro-processing system of modern semiconductor circuits is dependent on strategies organized on silicon chips to achieve the ... ...

    Abstract As a well-established technique, DNA synthesis offers interesting possibilities for designing multifunctional nanodevices. The micro-processing system of modern semiconductor circuits is dependent on strategies organized on silicon chips to achieve the speedy transmission of substances or information. Similarly, spatially localized structures allow for fixed DNA molecules in close proximity to each other during the synthesis of molecular circuits, thus providing a different strategy that of opening up a remarkable new area of inquiry for researchers. Herein, the Visual DSD (DNA strand displacement) modeling language was used to design and analyze the spatially organized DNA reaction network. The execution rules depend on the hybridization reaction caused by directional complementary nucleotide sequences. A series of DNA strand displacement calculations were organized on the locally coded travel track, and autonomous movement and addressing operations are gradually realized. The DNA nanodevice operates in this manner follows the embedded "molecular program", which improves the reusability and scalability of the same sequence domain in different contexts. Through the communication between various building blocks, the DNA device-carrying the target molecule moves in a controlled manner along the programmed track. In this way, a variety of molecular functional group transport and specific partition storage can be realized. The simulation results of the visual DSD tool provide qualitative and quantitative proof for the operation of the system.
    Mesh-Begriff(e) Computers, Molecular ; Computer Simulation ; DNA/chemistry ; Nucleic Acid Hybridization
    Chemische Substanzen DNA (9007-49-2)
    Sprache Englisch
    Erscheinungsdatum 2023-02-10
    Erscheinungsland Germany
    Dokumenttyp Journal Article
    ZDB-ID 2493085-4
    ISSN 1867-1462 ; 1913-2751
    ISSN (online) 1867-1462
    ISSN 1913-2751
    DOI 10.1007/s12539-023-00551-5
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  5. Artikel ; Online: A Biosensor Based on Interchain Reactions for the Detection of Acetamiprid and the Construction of Basic Logic Gates OR and AND.

    Hu, Mengyang / Wang, Luhui / Xi, Sunfan / Liu, Rong / Dong, Yafei

    IEEE transactions on nanobioscience

    2022  Band 21, Heft 3, Seite(n) 330–340

    Abstract: An enzyme-free and label-free fluorescent DNA aptasensor was constructed with computer assistance based on thermodynamic deviation driving interchain reactions. In this work, in the presence of target acetamiprid, the released trigger strand C-apt could ... ...

    Abstract An enzyme-free and label-free fluorescent DNA aptasensor was constructed with computer assistance based on thermodynamic deviation driving interchain reactions. In this work, in the presence of target acetamiprid, the released trigger strand C-apt could open hairpin Hp1, which in turn triggered the strand displacement reaction and catalyzed the self-assembly of hairpins Hp1 and Hp2, so that the guanine base rich stem in Hp2 was opened. In the presence of K
    Mesh-Begriff(e) Aptamers, Nucleotide ; Biosensing Techniques/methods ; Chromosomal Proteins, Non-Histone ; G-Quadruplexes ; Neonicotinoids
    Chemische Substanzen Aptamers, Nucleotide ; Chromosomal Proteins, Non-Histone ; Neonicotinoids ; acetamiprid (5HL5N372P0)
    Sprache Englisch
    Erscheinungsdatum 2022-06-30
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1558-2639
    ISSN (online) 1558-2639
    DOI 10.1109/TNB.2021.3139079
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  6. Buch ; Online: Target-oriented Domain Adaptation for Infrared Image Super-Resolution

    Huang, Yongsong / Miyazaki, Tomo / Liu, Xiaofeng / Dong, Yafei / Omachi, Shinichiro

    2023  

    Abstract: Recent efforts have explored leveraging visible light images to enrich texture details in infrared (IR) super-resolution. However, this direct adaptation approach often becomes a double-edged sword, as it improves texture at the cost of introducing noise ...

    Abstract Recent efforts have explored leveraging visible light images to enrich texture details in infrared (IR) super-resolution. However, this direct adaptation approach often becomes a double-edged sword, as it improves texture at the cost of introducing noise and blurring artifacts. To address these challenges, we propose the Target-oriented Domain Adaptation SRGAN (DASRGAN), an innovative framework specifically engineered for robust IR super-resolution model adaptation. DASRGAN operates on the synergy of two key components: 1) Texture-Oriented Adaptation (TOA) to refine texture details meticulously, and 2) Noise-Oriented Adaptation (NOA), dedicated to minimizing noise transfer. Specifically, TOA uniquely integrates a specialized discriminator, incorporating a prior extraction branch, and employs a Sobel-guided adversarial loss to align texture distributions effectively. Concurrently, NOA utilizes a noise adversarial loss to distinctly separate the generative and Gaussian noise pattern distributions during adversarial training. Our extensive experiments confirm DASRGAN's superiority. Comparative analyses against leading methods across multiple benchmarks and upsampling factors reveal that DASRGAN sets new state-of-the-art performance standards. Code are available at \url{https://github.com/yongsongH/DASRGAN}.

    Comment: 11 pages, 9 figures
    Schlagwörter Electrical Engineering and Systems Science - Image and Video Processing ; Computer Science - Computer Vision and Pattern Recognition
    Erscheinungsdatum 2023-11-15
    Erscheinungsland us
    Dokumenttyp Buch ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  7. Artikel: Potential Universal Engineering Component: Tetracycline Response Nanoswitch Based on Triple Helix-Graphene Oxide.

    Wang, Luhui / Wang, Yue / Hu, Mengyang / Xi, Sunfan / Liu, Rong / Cheng, Meng / Dong, Yafei

    Micromachines

    2022  Band 13, Heft 12

    Abstract: The overuse of antibiotics can lead to the emergence of drug resistance, preventing many common diseases from being effectively treated. Therefore, based on the special composite platform of P1/graphene oxide (GO) and DNA triple helix, a programmable DNA ...

    Abstract The overuse of antibiotics can lead to the emergence of drug resistance, preventing many common diseases from being effectively treated. Therefore, based on the special composite platform of P1/graphene oxide (GO) and DNA triple helix, a programmable DNA nanoswitch for the quantitative detection of tetracycline (TC) was designed. The introduction of GO as a quenching agent can effectively reduce the background fluorescence; stabilizing the trigger strand with a triplex structure minimizes errors. It is worth mentioning that the designed model has been verified and analyzed by both computer simulation and biological experiments. NUPACK predicts the combined mode and yield of each strand, while visual DSD flexibly predicts the changes in components over time during the reaction. The feasibility analysis preliminarily confirmed the realizability of the designed model, and the optimal reaction conditions were obtained through optimization, which laid the foundation for the subsequent quantitative detection of TC, while the selective experiments in different systems fully demonstrated that the model had excellent specificity.
    Sprache Englisch
    Erscheinungsdatum 2022-11-30
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article
    ZDB-ID 2620864-7
    ISSN 2072-666X
    ISSN 2072-666X
    DOI 10.3390/mi13122119
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  8. Artikel ; Online: Developing a DNA logic gate nanosensing platform for the detection of acetamiprid.

    Xi, Sunfan / Wang, Luhui / Cheng, Meng / Hu, Mengyang / Liu, Rong / Dong, Yafei

    RSC advances

    2022  Band 12, Heft 42, Seite(n) 27421–27430

    Abstract: This paper reports a novel fluorescence and colorimetric dual-signal-output DNA aptamer based sensor for the detection of acetamiprid residue. Acetamiprid is a new systemic broad-spectrum insecticide with high insecticidal efficiency that is widely used ... ...

    Abstract This paper reports a novel fluorescence and colorimetric dual-signal-output DNA aptamer based sensor for the detection of acetamiprid residue. Acetamiprid is a new systemic broad-spectrum insecticide with high insecticidal efficiency that is widely used worldwide, but there is a risk of adverse neurological reactions in humans and animals. The dual-mode output principle designed in this paper, consisting of a fluorescence signal and colorimetric signal, is based on the relevant reaction of the special domain of a G-quadruplex, bidding farewell to a classical single-signal output, with a target-recognition cycle used to complete signal amplification through a hybridization chain reaction. Upgraded detection sensitivity and the qualitative and semi-quantitative detection of acetamiprid are achieved based on the fluorescence signal output and visual discrimination observations during colorimetric experiments. This model was applied to the determination of acetamiprid residue in fruits and vegetables. The dual-detection platform further reduced systematic error, with a detection limit of 27.7 pM. When applied in a comparative detection study using three different pesticides, the system shows excellent discrimination specificity and it performs well in actual sample detection and has a fast response time. Designing DNA logic gates that operate in the presence of targets and molecular-switch-based detection platforms also involves the intersection of biology and computational modeling, providing new ideas for biological platforms.
    Sprache Englisch
    Erscheinungsdatum 2022-09-27
    Erscheinungsland England
    Dokumenttyp Journal Article
    ISSN 2046-2069
    ISSN (online) 2046-2069
    DOI 10.1039/d2ra04794b
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  9. Artikel ; Online: Development and analysis of a universal label-free micro/nano component for three-channel detection of silver ions, mercury ions, and tetracycline.

    Wang, Luhui / Hu, Mengyang / Liu, Rong / Xi, Sunfan / Cheng, Meng / Bao, Yangyinchun / Wang, Na / Dong, Yafei

    Analytica chimica acta

    2023  Band 1276, Seite(n) 341606

    Abstract: In this paper, an enzyme-free and label-free fluorescent nanomodule is proposed for rapid, simple and sensitive detection of ... ...

    Abstract In this paper, an enzyme-free and label-free fluorescent nanomodule is proposed for rapid, simple and sensitive detection of Ag
    Mesh-Begriff(e) Mercury/analysis ; Silver/analysis ; Ions ; DNA, Single-Stranded ; Anti-Bacterial Agents ; Tetracycline ; Heterocyclic Compounds
    Chemische Substanzen Mercury (FXS1BY2PGL) ; Silver (3M4G523W1G) ; Ions ; DNA, Single-Stranded ; Anti-Bacterial Agents ; Tetracycline (F8VB5M810T) ; Heterocyclic Compounds
    Sprache Englisch
    Erscheinungsdatum 2023-07-08
    Erscheinungsland Netherlands
    Dokumenttyp Journal Article
    ZDB-ID 1483436-4
    ISSN 1873-4324 ; 0003-2670
    ISSN (online) 1873-4324
    ISSN 0003-2670
    DOI 10.1016/j.aca.2023.341606
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  10. Artikel: Developing a three-input cascade DNA logic gate based on the biological characteristics of metal ion–GO, combined with analysis and verification

    Wang, Luhui / Hu, Mengyang / Wang, Yue / Xi, Sunfan / Cheng, Meng / Niu, Li / Dong, Yafei

    Analytical methods. 2021 Oct. 28, v. 13, no. 41

    2021  

    Abstract: Due to the limitation of technology, electronic computing is approaching the limit of technology, and new computing tools need to be developed. Here, we build a three-input cascade logic gate based on the advantages of biomolecules, particularly DNA, in ... ...

    Abstract Due to the limitation of technology, electronic computing is approaching the limit of technology, and new computing tools need to be developed. Here, we build a three-input cascade logic gate based on the advantages of biomolecules, particularly DNA, in the construction of computational logic systems, combined with metal ions and graphene oxide (GO). It is worth mentioning that this study uses a variety of research methods. In addition to the commonly used biological experiments, NUPACK and visual DSD simulation methods are used for analysis, and orthogonal, standardized and other statistical means are used to simplify the experimental process and make the results intuitive. Finally, the designed three-input logic gate is successfully constructed, and it is found that it may have the potential to realize complex computing.
    Schlagwörter DNA ; analytical methods ; graphene oxide ; metal ions ; metals ; research methods
    Sprache Englisch
    Erscheinungsverlauf 2021-1028
    Umfang p. 4955-4963.
    Erscheinungsort The Royal Society of Chemistry
    Dokumenttyp Artikel
    ZDB-ID 2515210-5
    ISSN 1759-9679 ; 1759-9660
    ISSN (online) 1759-9679
    ISSN 1759-9660
    DOI 10.1039/d1ay01309b
    Datenquelle NAL Katalog (AGRICOLA)

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