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作者： qian, shuwen McMaster University

学位级别：博士

The functionality of nucleic acids beyond genetics has attracted more attention over the past decades. Functional nucleic acids (FNA), including aptamers and nucleic acid-based enzymes, are well-known for their target binding and reaction catalysis abilities. FNA can be obtained through a technology called in vitro selection, which allows the isolation of customized FNA for various applications. In particular, FNA have received much interest in biosensing application. Their wide range of sensing targets, intrinsic stability, and high specificity have qualified them as the molecular recognition element in biosensors. This thesis explored the utilization of FNA to tackle real-world biosensing challenges, especially for pathogenic bacteria detection. The first project aimed to make the most use of in vitro selection to derive FNA that can meet the requirements of terminal applications. A few feasible approaches were proposed based on lessons from Mother Nature and validated by innovative scientist pioneers. In the second research project, I characterized an RNA-cleaving DNAzyme for Clostridium difficile infection diagnosis. This DNAzyme displayed high sensitivity and specificity for clinical C. difficile strains, making it a competitive candidate for a potential point-of-care diagnostic tool. In the next chapter, I incorporated a Legionella pneumophila-responsive RNA-cleaving DNAzyme into a bead-based assay for practical on-site detection. This assay exhibited a high stability and functionality in the cooling tower water samples, the real-world application environment. The following chapter was to optimize this assay further with a coupled rolling circle amplification strategy. This additional amplification speeded up the detection process, improved the limit of detection, and enabled the colorimetric results that are observable to the naked eye. These research aimed to advance the practical applications of FNA as key components in biosensors. I hope readers find thi

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Dynamic moisture sorption and humidity response inside the wooden space to cyclical changing external relative humidity

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WOOD MATERIAL SCIENCE & ENGINEERING 2023年第6期18卷 1922-1932页

作者： Yang, Tiantian Mei, Changtong qian, shuwen Nanjing Forestry Univ Coll Mat Sci & Engn Nanjing Peoples R China Nanjing Forestry Univ Coinnovat Ctr Efficient Proc & Utilizat Forest Res Nanjing Peoples R China Nanjing Forestry Univ Coll Mat Sci & Engn Nanjing 210037 Peoples R China Nanjing Forestry Univ Coinnovat Ctr Efficient Proc & Utilizat Forest Res Nanjing 210037 Peoples R China

Wood is usually processed into various spaces and used in buildings, packaging and furniture. Dynamic moisture sorption and humidity response inside wooden space to sinusoidally changing external relative humidity (RH) were demonstrated by using a self-assembly device, which simultaneously recorded moisture content (MC) and RH changes. Wood has hierarchical structures, which provided the basis of moisture sorption and further influenced RH inside. Internal RH changed sinusoidally, similar to external RH and MC. During internal and external moisture exchange, water molecules experienced dynamic compound actions, including moisture gradient pressure, the attraction of sorption sites and water molecules and diffusing hindrance. Consequently, MC and internal RH exhibited dynamic phase lag of over 0.39 radian. Meanwhile, moisture sorption was higher for thinner wood, especially in a longer cyclic period since more water molecules interacted with sorption sites with less diffusing hindrance. Correspondingly, the humidity change was lower inside thicker wooden spaces in a shorter period. The average internal RH and amplitude decreased by 5% and 83.7%, respectively. Dynamic humidity change hysteresis existed and showed positive relation to the cyclic period but inversely with wood thickness. The study helped better understand dynamic moisture sorption and humidity change in wooden space and facilitated the better application of wood in human life.

关键词： Cyclical humidity change dynamic humidity response dynamic moisture sorption wood

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Data-Driven Stiffness Modeling and Design Optimization of Flexible Backbones for Modular Cable-Driven Continuum Robots

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IEEE TRANSACTIONS ON INDUSTRIAL INFORMATICS 2025年第4期21卷 3137-3146页

作者： Shen, Wenjun Yang, Guilin He, Jianhui qian, shuwen Bai, Haotian Zheng, Tianjiang Fang, Zaojun Ningbo Inst Mat Technol & Engn Ningbo 315201 Peoples R China Univ Nottingham Ningbo 315100 Peoples R China

Most bioinspired cable-driven continuum robots (CDCRs) usually employ a flexible backbone to realize the continuous deflection. For the CDCR to merely produce bending motions, its flexible backbone has to be designed with low bending stiffness but high tensile and torsion stiffness. In this article, a pattern-based design approach is employed for the flexible backbone, which adopts rectangle-shaped patterns inspired by elastic couplings. As it is rather difficult to derive accurate analytical stiffness models for such a pattern-based backbone structure with large nonlinear deflections, a novel data-driven stiffness modeling approach is proposed. The Gaussian process regression method is employed to train the stiffness model with respect to structure parameters of the backbone, while the dataset is generated through a commercial finite element analysis software package. To narrow the distribution of the training data and make the predicated stiffness values always positive, the natural logarithm transformation is utilized for data preprocessing, which significantly increases the accuracy of prediction results. The average errors of the bending, tensile, and torsion stiffness between simulation results and predicted results converge to 1.88%, 2.33%, and 2.11%, respectively. The particle swarm optimization algorithm is employed for the structure parameter optimization based on the data-driven stiffness model. The stiffness errors of the optimized flexible backbone between simulation results and experimental results are 5.19%, 19.09%, and 5.38%, respectively. Experimental results show that the average position repeatability and orientation repeatability of a CDCR are 0.8822 mm and 0.0046 rad and the CDCR can carry the 500 g payload.

关键词： Bending Analytical models Training data Shape Continuum robots Adaptation models Accuracy Training Stability analysis Solid modeling Cable-driven continuum robot (CDCR) data-driven stiffness modeling flexible backbone structure parameter optimization

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Feedback Control of Cable-Driven Continuum Robot Based on Flexible Perception

Feedback Control of Cable-Driven Continuum Robot Based on Fl...

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2022 International Conference on Mathematics, Modeling, and Computer Science, MMCS 2022

作者： qian, shuwen Zheng, Tianjiang Shen, Wenjun Ningbo Institute of Materials Technology Engineering Chinese Academy of Sciences Ningbo China University of Chinese Academy of Sciences Beijing China Zhejiang Key Laboratory of Robotics and Intelligent Manufacturing Equipment Technology Ningbo China

ISBN: (纸本)9781510664593

Aiming at the problems of limited accuracy of model and poor position control precision caused by complex deformation of Cable-Driven Continuum Robot(CDCR), a shape sensing and feedback control approach for CDCR is proposed based on the elastic magnetoelectric strain sensor. Kinematic model of robot was established based on the product of exponential (POE) formula. Based on physical characteristics of the sensor, the shape sensing model of the robot was proposed and Qualisys Track System was used for calibration. A module prototype was built to verify the effect of the perceptual feedback control algorithm. The experiment proves that the flexible perception method used in this paper is universal and accurate, and provides a valuable framework for real-time sensing control. © 2023 SPIE.

关键词： Cables

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Compound Probiotics Improve Neuropathic Pain Prognosis in a Murine Model of Chronic Constriction Injury

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JOURNAL OF PAIN RESEARCH 2024年 17卷 4213-4221页

作者： Wang, Xiaomei Chen, Yinsheng qian, shuwen Kong, Jia Su, Zehua Wang, Qingxiu Liao, Lijun Shanghai Jiao Tong Univ Xinhua Hosp Sch Med Dept Anesthesiol Shanghai Peoples R China Shanghai Jiao Tong Univ Xinhua Hosp Sch Med Surg Intens Care Unit Shanghai Peoples R China Tongji Univ Shanghai East Hosp Sch Med Dept Anesthesiol Management Shanghai Peoples R China Nanjing Med Univ Shanghai East Hosp Clin Med Coll 1800 YunTai Rd Shanghai 200123 Peoples R China Tongji Univ Yangpu Hosp Sch Med Dept Anesthesiol & Pain Management Shanghai Peoples R China Tongji Univ Shanghai East Hosp Sch Med Dept Pain Management 1800 Yuntai Rd Shanghai 200123 Peoples R China

Purpose: Compound probiotics have been reported to ameliorate imbalances in the intestinal flora that may play a critical role in neuropathic pain. This study aimed to investigate the efficacy of compound probiotic treatment on neuropathic pain. Methods: Thirty mice were randomly divided into three groups: 1) sham group, 2) mouse with chronic constrictive injury (CCI), and 3) probiotic gavage with CCI (CCI+Prob). The degree of pain and gait recovery was assessed by Mechanical withdrawal threshold (MWT), thermal withdrawal latency (TWL), and mouse footprints. The degree of atrophy of the gastrocnemius muscle was assessed by muscle weight, hematoxylin and eosin (H&E) staining. Gut microbiota were analyzed by 16S ribosomal RNA sequencing (16SrRNA). Results: Four weeks after surgery, TWL and MWT assessment showed significant increases in the CCI+Prob group compared with the CCI group (P < 0.01). Gait analysis results as well as gastrocnemius muscle weight showed a significant improvement in the CCI +Prob group compared with the CCI group. Measurement of alpha diversity showed a significant increase in the CCI group compared with the sham group, but this increase was attenuated by probiotic intervention in the CCI+Prob group. Although the CCI group had significantly decreased levels of Akkermansia and significantly increased levels of Ruminococcaceae, probiotic treatment reversed these changes. Conclusion: Compound probiotics treatment can improve the pain and muscle atrophy in mice with CCI-induced neuropathic pain. The improvement of symptoms is associated with changes in the composition of gut microbiota.

关键词： probiotics neuropathic pain gut microbiota muscle atrophy Akkermansia Ruminococcaceae

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Feedback Control of Cable-Driven Continuum Robot based on flexible perception 2

Feedback Control of Cable-Driven Continuum Robot based on fl...

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2nd International Symposium on Control Engineering and Robotics, ISCER 2023

作者： qian, shuwen Zheng, Tianjiang Shen, Wenjun Bai, Haotian Ningbo Institute of Materials Technology and Engineering Chinese Academy of Sciences Ningbo China University of Chinese Academy of Sciences Beijing China Key Laboratory of Robotics and Intelligent Equipment Technology of Zhejiang Province Ningbo China University of Nottingham Ningbo China

ISBN: (纸本)9798350336405

Aiming at problems of the limited accuracy of the model and poor control precision caused by the complex deformation of Cable-Driven Continuum Robot(CDCR), a shape sensing and feedback control approach for CDCR is proposed based on the elastic magnetoelectric strain sensor. The kinematic model of CDCR was established based on the product of the exponential (POE) formula. Based on the sensor's physical characteristics, the robot's shape-sensing model was proposed and Qualisys Track System was used for calibration. A module prototype was built to verify the effect of the perceptual feedback control algorithm. The experiment proved that the flexible perception method used in this paper is universal and accurate, and provides a valuable framework for real-time sensing control. © 2023 IEEE.

关键词： Feedback control

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Electrochemical detection of Legionella pneumophila using DNAzymes and under continuous flow in cooling tower water

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BIOSENSORS & BIOELECTRONICS 2025年 278卷 117283页

作者： Osman, Enas Saxena, Survanshu qian, shuwen L'Heureux-Hache, Jonathan Li, Phoebe Manek, Jinal Gu, Jimmy Hoare, Todd Li, Yingfu Soleymani, Leyla McMaster Univ Sch Biomed Engn Hamilton ON L8S 4L8 Canada McMaster Univ Dept Biochem & Biomed Sci Hamilton ON L8S 4L8 Canada McMaster Univ Dept Engn Phys Hamilton ON L8S 4L8 Canada McMaster Univ Dept Chem Engn Hamilton ON L8S 4L8 Canada McMaster Univ Michael G DeGroote Inst Infect Dis Res Hamilton ON L8S 4L8 Canada

Rapid detection of Legionella pneumophila in cooling tower water is crucial to mitigate the fatal consequences of Legionnaires disease. This study presents a microfluidic system that employs RNA-cleaving DNAzymes (RCDs) for continuous real time monitoring of this pathogen directly in a single sample of cooling tower water without the need for lengthy bacterial culture. The RCDs, coupled to microgel magnetic beads, are programmed to release an electroactive DNA barcode in the presence of L. pneumophila, which is detected by a downstream electrochemical sensor in real time. Our system identifies key parameters such as peak current, slope of signal increase, and lag time that correlate with L. pneumophila concentration, achieving a limit of detection of 1.4 x 103 CFU/mL in buffer and 1.9 x 103 CFU/mL in cooling tower water, meeting regulatory requirements. This system was further used to identify different serotypes of L. pneumophila amongst other waterborne bacterial species including non pneumophila species of Legionella, creating a highly specific tool for identifying this high-risk pathogen.

关键词： Biosensing DNAzyme Microfluidics Bacterial detection Legionella pneumophila

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Aptamers from random sequence space: Accomplishments, gaps and future considerations

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ANALYTICA CHIMICA ACTA 2022年 1196卷 339511-339511页

作者： qian, shuwen Chang, Dingran He, Sisi Li, Yingfu McMaster Univ Michael G DeGroote Inst Infect Dis Res Dept Biochem & Biomed Sci 1280 Main St West Hamilton ON L8S 4K1 Canada McMaster Univ Dept Chem & Chem Biol 1280 Main St West Hamilton ON L8S 4K1 Canada Harbin Inst Technol Shenzhen Sch Sci Shenzhen 518055 Guangdong Peoples R China

Aptamers are molecular recognition elements made of nucleic acids. Diverse synthetic aptamers have been discovered in a large number of SELEX experiments since 1990. This review begins with the analysis of these SELEX experiments by examining the range of targets as well as the affinity and specificity for these targets by DNA, RNA or modified nucleic acid aptamers generated from these experiments. This is followed by comparisons of synthetic aptamers with natural RNA aptamers from riboswitches and with some of the best naturally occurring protein based recognition elements for proteins and small molecules. These comparisons reveal the gaps between man-made aptamers and natural recognition elements. We then put forward a series of ideas for consideration by the aptamer community towards developing better aptamers to solve real world problems. These include performing aptamer selections with libraries containing larger random sequence domains to derive larger aptamers with more intricate structures, conducting more reselection experiments using mutagenized DNA libraries based on initially selected aptamer sequences to search for better members of an aptamer family, selecting aptamers that are programmed to recognize two or more different epitopes of the same target in order to build multivalent aptamers for increased affinity, expanding the effort of selecting aptamers using modified nucleic acids with enhanced chemical functionalities, innovating SELEX methods to drive for the selection of aptamers with truly outstanding affinity and specificity, and having terminal applications in mind when creating new aptamers so that they are highly functional in the environment where the applications are planned. (c) 2022 Elsevier B.V. All rights reserved.

关键词： Aptamers SELEX In vitro selection DNA RNA Modified nucleic acids

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In Vitro Selection and Characterization of a DNAzyme Probe for Diverse Pathogenic Strains of Clostridium difficile

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CHEMISTRY-A EUROPEAN JOURNAL 2023年第36期29卷 e202300240-e202300240页

作者： qian, shuwen Chang, Dingran Gu, Jimmy Salena, Bruno J. Li, Yingfu McMaster Univ Dept Biochem & Biomed Sci 1280 Main St West Hamilton ON L8S 4K1 Canada McMaster Univ Dept Med 1280 Main St West Hamilton ON L8S 4K1 Canada McMaster Univ Michael G DeGroote Inst Infect Dis Res 1280 Main St West Hamilton ON L8S 4K1 Canada McMaster Univ Sch Biomed Engn 1280 Main St West Hamilton ON L8S 4K1 Canada McMaster Univ Biointerfaces Inst 1280 Main St West Hamilton ON L8S 4K1 Canada

Clostridium difficile frequently causes an infectious disease known as Clostridium difficile infection (CDI), and there is an urgent need for the development of more effective rapid diagnostic tests for CDI. Previously we have developed an RNA-cleaving fluorogenic DNAzyme (RFD) probe, named RFD-CD1, that is capable of detecting a specific strain of C. difficile but is too specific to recognize other pathogenic C. difficile strains. To overcome this issue, herein we report RFD-CD2, another RFD that is not only highly specific to C. difficile but also capable of recognizing diverse pathogenic C. difficile strains. Extensive sequence and structure characterization establishes a pseudoknot structure and a significantly minimized sequence for RFD-CD2. As a fluorescent sensor, RFD-CD2 can detect C. difficile at a concentration as low as 100 CFU/mL, thus making this DNAzyme an attractive molecular probe for rapid diagnosis of CDI caused by diverse strains of C. difficile.

关键词： biosensors Clostridium difficile DNAzymes fluorescent probes pseudoknots

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Feedback Control of Cable-Driven Continuum Robot based on flexible perception

Feedback Control of Cable-Driven Continuum Robot based on fl...

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Control Engineering and Robotics (ISCER), International Symposium on

作者： shuwen qian Tianjiang Zheng Wenjun Shen Haotian Bai Chinese Academy of Sciences Ningbo Institute of Materials Technology and Engineering Ningbo China University of Chinese Academy of Sciences Beijing China Key Laboratory of Robotics and Intelligent Equipment Technology of Zhejiang Province Ningbo China University of Nottingham Ningbo China

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