103 results on '"Yuxuan Cheng"'
Search Results
2. Causal associations between gut microbiota, circulating inflammatory proteins, and epilepsy: a multivariable Mendelian randomization study
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Han Yang, Wei Liu, Tiantian Gao, Qifan Liu, Mengyuan Zhang, Yixin Liu, Xiaodong Ma, Nan Zhang, Kaili Shi, Minyu Duan, Shuyin Ma, Xiaodong Zhang, Yuxuan Cheng, Huiyang Qu, Mengying Chen, and Shuqin Zhan
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gut microbiota ,epilepsy ,inflammatory proteins ,Mendelian randomization ,microbiota-gut-brain-axis ,Immunologic diseases. Allergy ,RC581-607 - Abstract
BackgroundPrevious studies have suggested that gut microbiota (GM) may be involved in the pathogenesis of epilepsy through the microbiota-gut-brain axis (MGBA). However, the causal relationship between GM and different epilepsy subtypes and whether circulating inflammatory proteins act as mediators to participate in epileptogenesis through the MGBA remain unclear. Therefore, it is necessary to identify specific GM associated with epilepsy and its subtypes and explore their underlying inflammatory mechanisms for risk prediction, personalized treatment, and prognostic monitoring of epilepsy.MethodsWe hypothesized the existence of a pathway GM-inflammatory proteins-epilepsy. We found genetic variants strongly associated with GM, circulating inflammatory proteins, epilepsy and its subtypes, including generalized and partial seizures, from large-scale genome-wide association studies (GWAS) summary data and used Multivariate Mendelian Randomization to explore the causal relationship between the three and whether circulating inflammatory proteins play a mediating role in the pathway from GM to epilepsy, with inverse variance weighted (IVW) method as the primary statistical method, supplemented by four methods: MR-Egger, weighted median estimator (WME), Weighted mode and Simple mode.Results16 positive and three negative causal associations were found between the genetic liability of GM and epilepsy and its subtypes. There were nine positive and nine negative causal associations between inflammatory proteins and epilepsy and its subtypes. Furthermore, we found that C-X-C motif chemokine 11 (CXCL11) levels mediated the causal association between Genus Family XIII AD3011 group and epilepsy.ConclusionOur study highlights the possible causal role of specific GM and specific inflammatory proteins in the development of epilepsy and suggests that circulating inflammatory proteins may mediate epileptogenesis through the MGBA.
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- 2024
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3. Longitudinal SS-OCT choroidal imaging following thrombosis of the superior ophthalmic vein
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Mengxi Shen, Prashanth G. Iyer, Hao Zhou, Yuxuan Cheng, Jeremy Liu, Omer Trivizki, Ruikang K. Wang, Giovanni Gregori, and Philip J. Rosenfeld
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Superior ophthalmic vein thrombosis ,Swept-source optical coherence tomography ,Choroidal thickness ,Choroidal vascular index ,Choroidal vasculature ,Choroidal outflow obstruction ,Ophthalmology ,RE1-994 - Abstract
Purpose: To report longitudinal changes in choroidal thickness and the choroidal vasculature using SS-OCT imaging in a patient with superior ophthalmic vein thrombosis (SOVT). Observations: In a 93-year-old woman with a left-sided SOVT, the choroid in the left eye was thickened and the choroidal vessels were dilated both superiorly and inferiorly, with greater changes evident in the inferotemporal region of the choroid. After the superior ophthalmic vein was decompressed, a decrease in the choroidal thickness and choroidal vessel dilatation was observed both superiorly and inferiorly. Conclusions and importance: In an eye with thrombosis of the superior ophthalmic vein, longitudinal SS-OCT choroidal imaging showed a greater increase in choroidal thickness and choroidal vessel dilation away from the obstructed quadrant, which improved after treatment. These observations associated with outflow obstruction may be applicable to other choroidal diseases characterized by venous overload.
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- 2024
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4. Safety-Centric Precision Control of a Modified Duodenoscope Designed for Surgical Robotics
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Yuxuan Cheng, Ruyan Yan, Bingyi Liu, Chun Yang, and Tianyu Xie
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robotic-assisted surgery ,duodenoscope ,forward control ,Tendon-Sheath-Mechanism (TSM) ,Mechanical engineering and machinery ,TJ1-1570 - Abstract
There is limited research on robotic systems designed for Endoscopic Retrograde Cholangiopancreatography (ERCP) procedures using a side-view duodenoscope. The unique structure of the duodenoscope presents challenges to safely and precisely control the distal end pose. Control methods applied can reduce potential medical risks. We have redesigned the control section of the duodenoscope to facilitate its manipulation by a robotic system. An orthogonal compensator is employed to rectify the motion planes to standard planes. A hysteresis compensator based on the Prandtl-Ishlinskii model enables precise control of the distal pose of the duodenoscope. Furthermore, we utilize a contact force prediction model to prevent excessive contact force at the distal end. The performance of the modified duodenoscope is comparable to that of the standard duodenoscope. Following orthogonal compensation, the deviation angles of the motion planes is reduced by 32% to 98%. Post-hysteresis compensation, the root mean square error (RMSE) of the output angle of the distal end is decreased from 8.347° to 4.826°. The accuracy of distal end contact force prediction was approximately ±25% under conditions of high contact force. In conclusion, the modification and control strategy we proposed can achieve relatively safe and precise control of bending section, laying the foundation for the subsequent roboticization of duodenoscope systems for ERCP procedures.
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- 2024
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5. Robust Detection of Cracked Eggs Using a Multi-Domain Training Method for Practical Egg Production
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Yuxuan Cheng, Yidan Huang, Jingjing Zhang, Xuehong Zhang, Qiaohua Wang, and Wei Fan
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cracked egg ,unknown egg test domain ,multi-domain training ,MMD ,robust ,efficient ,Chemical technology ,TP1-1185 - Abstract
The presence of cracks reduces egg quality and safety, and can easily cause food safety hazards to consumers. Machine vision-based methods for cracked egg detection have achieved significant success on in-domain egg data. However, the performance of deep learning models usually decreases under practical industrial scenarios, such as the different egg varieties, origins, and environmental changes. Existing researches that rely on improving network structures or increasing training data volumes cannot effectively solve the problem of model performance decline on unknown egg testing data in practical egg production. To address these challenges, a novel and robust detection method is proposed to extract max domain-invariant features to enhance the model performance on unknown test egg data. Firstly, multi-domain egg data are built on different egg origins and acquisition devices. Then, a multi-domain trained strategy is established by using Maximum Mean Discrepancy with Normalized Squared Feature Estimation (NSFE-MMD) to obtain the optimal matching egg training domain. With the NSFE-MMD method, the original deep learning model can be applied without network structure improvements, which reduces the extremely complex tuning process and hyperparameter adjustments. Finally, robust cracked egg detection experiments are carried out on several unknown testing egg domains. The YOLOV5 (You Only Look Once v5) model trained by the proposed multi-domain training method with NSFE-MMD has a detection mAP of 86.6% on the unknown test Domain 4, and the YOLOV8 (You Only Look Once v8) model has a detection mAP of 88.8% on Domain 4, which is an increase of 8% and 4.4% compared to the best performance of models trained on a single domain, and an increase of 4.7% and 3.7% compared to models trained on all domains. In addition, the YOLOV5 model trained by the proposed multi-domain training method has a detection mAP of 87.9% on egg data of the unknown testing Domain 5. The experimental results demonstrate the robustness and effectiveness of the proposed multi-domain training method, which can be more suitable for the large quantity and variety of egg detection production.
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- 2024
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6. Longitudinal quantification of choriocapillaris flow deficits in persistent placoid maculopathy: a case report
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Jianqing Li, Chris Y. Wu, Mengxi Shen, Leon Bynoe, Joseph Nezgoda, Jeremy Liu, Yuxuan Cheng, Anna Sporysheva, Thomas Albini, Ruikang K. Wang, Giovanni Gregori, and Philip J. Rosenfeld
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Persistent placoid maculopathy ,Choriocapillaris flow deficits ,Optical coherence tomography ,Swept source optical coherence tomography angiography ,Ophthalmology ,RE1-994 - Abstract
Abstract Background Persistent placoid maculopathy (PPM) is a rare idiopathic chorioretinopathy characterized by choriocapillaris (CC) hypoperfusion. In a case of PPM, we quantified CC flow deficits (FDs) over time and observed an increase in CC perfusion as the visual acuity and outer photoreceptor anatomy improved. Case presentation A 58-year-old man was diagnosed with PPM in both eyes based on the patient’s clinical presentation and imaging. He presented with sudden-onset central scotomas in both eyes for about two months. On referral, the best corrected visual acuity (BCVA) was 20/20 in the right eye and 20/100 in the left eye. Plaque-like yellowish macular lesions were observed bilaterally and autofluorescence imaging showed bilateral hyperautofluorescent lesions. Fluorescein angiography (FA) revealed early-phase hyper-fluorescent staining that intensified in the late phases, while indocyanine green angiography (ICGA) displayed persistent hypofluorescence in both eyes. Foveal centered swept source optical coherence tomography (SS-OCT) B-scans showed bilateral focal deposits on the level of retinal pigment epithelium (RPE) and disruption of outer photoreceptor bands. The CC FDs were quantified on SS-OCT angiography (SS-OCTA) images using a previously published algorithm that was validated. The CC FD% was 12.52% in the right eye and 14.64% in the left eye within a 5 mm circle centered on the fovea. After 5 months of steroid treatment, BCVA remained 20/20 in the right eye and improved to 20/25 in the left eye. On OCT imaging, the outer photoreceptor bands fully recovered in both eyes, while some focal deposits remained along the RPE in the left eye. The CC perfusion in both eyes improved, with CC FD% decreasing from 12.52% to 9.16% in the right eye and from 14.64% to 9.34% in the left eye. Conclusions Significant impairment of macular CC perfusion was detected after the onset of PPM. Improvement in central macular CC perfusion corresponded with improvements in BCVA and outer retinal anatomy. Our findings suggest that imaging and quantification of CC FDs could serve as a valuable imaging strategy for diagnosing PPM and for following disease progression.
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- 2023
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7. Comparison between Spectral-Domain and Swept-Source OCT Angiography for the Measurement of Persistent Hypertransmission Defects in Age-Related Macular Degeneration
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Gissel Herrera, MD, Mengxi Shen, MD, PhD, Omer Trivizki, MD, Jeremy Liu, MD, Yingying Shi, MD, Farhan E. Hiya, MD, Jianqing Li, MD, Yuxuan Cheng, BS, Jie Lu, MD, MS, Qinqin Zhang, PhD, Robert C. O’Brien, PhD, Giovanni Gregori, PhD, Ruikang K. Wang, PhD, and Philip J. Rosenfeld, MD, PhD
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Age-related macular degeneration (AMD) ,En face imaging ,Persistent choroidal hypertransmission defects (HyperTDs) ,Spectral-domain OCT angiography (SD-OCTA) ,Swept-source OCT angiography (SS-OCTA) ,Ophthalmology ,RE1-994 - Abstract
Purpose: Spectral-domain OCT angiography (SD-OCTA) scans were tested in an algorithm developed for use with swept-source OCT angiography (SS-OCTA) scans to determine if SD-OCTA scans yielded similar results for the detection and measurement of persistent choroidal hypertransmission defects (hyperTDs). Design: Retrospective study. Participants: Forty pairs of scans from 32 patients with late-stage nonexudative age-related macular degeneration (AMD). Methods: Patients underwent both SD-OCTA and SS-OCTA imaging at the same visit using the 6 × 6 mm OCTA scan patterns. Using a semiautomatic algorithm that helped with outlining the hyperTDs, 2 graders independently validated persistent hyperTDs, which are defined as having a greatest linear dimension ≥250 μm on the en face images generated using a slab extending from 64 to 400 μm beneath Bruch’s membrane. The number of lesions and square root (sqrt) total area of the hyperTDs were obtained from the algorithm using each imaging method. Main Outcome Measures: The mean sqrt area measurements and the number of hyperTDs were compared. Results: The number of lesions and sqrt total area of the hyperTDs were highly concordant between the 2 instruments (rc = 0.969 and rc = 0.999, respectively). The mean number of hyperTDs was 4.3 ± 3.1 for SD-OCTA scans and 4.5 ± 3.3 for SS-OCTA scans (P = 0.06). The mean sqrt total area measurements were 1.16 ± 0.64 mm for the SD-OCTA scans and 1.17 ± 0.65 mm for the SS-OCTA scans (P < 0.001). Because of the small standard error of the differences, the mean difference between the scans was statistically significant but not clinically significant. Conclusions: Spectral-domain OCTA scans provide similar results to SS-OCTA scans when used to obtain the number and area measurements of persistent hyperTDs through a semiautomated algorithm previously developed for SS-OCTA. This facilitates the detection of atrophy with a more widely available scan pattern and the longitudinal study of early to late-stage AMD. Financial Disclosure(s): Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.
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- 2025
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8. Identification of a ferroptosis-related gene pair biomarker with immune infiltration landscapes in ischemic stroke: a bioinformatics-based comprehensive study
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Jiaxin Fan, Mengying Chen, Shuai Cao, Qingling Yao, Xiaodong Zhang, Shuang Du, Huiyang Qu, Yuxuan Cheng, Shuyin Ma, Meijuan Zhang, Yizhou Huang, Nan Zhang, Kaili Shi, and Shuqin Zhan
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Ischemic stroke ,Ferroptosis ,Gene pair ,Immune infiltration ,Biomarker ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Ischemic stroke (IS) is a principal contributor to long-term disability in adults. A new cell death mediated by iron is ferroptosis, characterized by lethal aggregation of lipid peroxidation. However, a paucity of ferroptosis-related biomarkers early identify IS until now. This study investigated potential ferroptosis-related gene pair biomarkers in IS and explored their roles in immune infiltration. Results In total, we identified 6 differentially expressed ferroptosis-related genes (DEFRGs) in the metadata cohort. Of these genes, 4 DEFRGs were incorporated into the competitive endogenous RNA (ceRNA) network, including 78 lncRNA-miRNA and 16 miRNA-mRNA interactions. Based on relative expression values of DEFRGs, we constructed gene pairs. An integrated scheme consisting of machine learning algorithms, ceRNA network, and gene pair was proposed to screen the key DEFRG biomarkers. The receiver operating characteristic (ROC) curve witnessed that the diagnostic performance of DEFRG pair CDKN1A/JUN was superior to that of single gene. Moreover, the CIBERSORT algorithm exhibited immune infiltration landscapes: plasma cells, resting NK cells, and resting mast cells infiltrated less in IS samples than controls. Spearman correlation analysis confirmed a significant correlation between plasma cells and CDKN1A/JUN (CDKN1A: r = − 0.503, P
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- 2022
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9. A Job Recommendation Method Based on Attention Layer Scoring Characteristics and Tensor Decomposition
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Yu Mao, Yuxuan Cheng, and Chunyu Shi
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job recommendation system ,tensor decomposition ,multi-source heterogeneous data ,user attention hierarchy ,Technology ,Engineering (General). Civil engineering (General) ,TA1-2040 ,Biology (General) ,QH301-705.5 ,Physics ,QC1-999 ,Chemistry ,QD1-999 - Abstract
In the field of job recruitment, a classic recommendation system consists of users, positions, and user ratings on positions. Its key task is to predict the unknown rating data of users on positions and then recommend positions that users are interested in. However, traditional recommendation methods only rely on user rating data for jobs and provide recommendation services for recruiters and candidates through simple information matching. This simple recommendation strategy not only causes a lot of information waste but also cannot effectively utilize the multi-source heterogeneous data information in the field of job recruitment. Therefore, this paper proposes a job recommendation model based on users’ attention levels and tensor decomposition for specific recruitment positions. This model puts forward assumptions based on browsing time for the special behaviors and habits of users in the field of job recruitment, defines corresponding label values for different interactive behaviors, and establishes a grading method based on the attention of job seekers, thus constructing a three-dimensional tensor of “job seeker user-position-attention layered”. Then, a recommendation model is constructed by decomposing the three-dimensional tensor. The effectiveness of the model is verified by comparative experiments with other recommendation algorithms.
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- 2023
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10. A preliminary investigation of amino acid and acylcarnitine levels in neonates from the Tibet autonomous
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Chunyan Zhang, Drun Dha, Yuxuan Cheng, Ya Ma, Yan Meng, Drun Tse, Dolma Ngawang, Pedrun Dekyi, Tao Jiang, Yang Shu, Jiayi Cui, Jing Li, and Yaping Tian
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amino acid ,acyl carnitine ,newborn screening ,Tibet region ,reference interval ,tandem mass spectrometry ,Genetics ,QH426-470 - Abstract
Background: The purpose of the study was to investigate the levels of amino acids and acylcarnitines in newborns of the Tibet Autonomous Region for the first time and to provide an experimental basis for the diagnosis of genetic metabolic diseases.Methods: We detected concentrations of 43 kinds of amino acids, acylcarnitines and succinylacetone in the dried blood spots of 18482 newborns using liquid chromatography tandem mass spectrometry and diagnose the case by gene sequencing. We compared the indexes between Tibet and our lab, where most data come from an inland area and Han Chinese people. Then we compared amino acid and acylcarnitine levels of seven regions in Tibet and explored their impact factors.Results: We described the levels of amino acids and acylcarnitines in Tibet newborns using 95% confidence intervals. The distribution of amino acid and acylcarnitines were different in Tibet.Conclusion: This study has contributed to filling in the blanks of Tibet newborn screening, which should be considered in the newborn metabolic disease screening in this area.
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- 2022
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11. The prediction of asymptomatic carotid atherosclerosis with electronic health records: a comparative study of six machine learning models
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Jiaxin Fan, Mengying Chen, Jian Luo, Shusen Yang, Jinming Shi, Qingling Yao, Xiaodong Zhang, Shuang Du, Huiyang Qu, Yuxuan Cheng, Shuyin Ma, Meijuan Zhang, Xi Xu, Qian Wang, and Shuqin Zhan
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Machine learning ,Asymptomatic carotid atherosclerosis ,Electronic health records ,Prediction ,Computer applications to medicine. Medical informatics ,R858-859.7 - Abstract
Abstract Background Screening carotid B-mode ultrasonography is a frequently used method to detect subjects with carotid atherosclerosis (CAS). Due to the asymptomatic progression of most CAS patients, early identification is challenging for clinicians, and it may trigger ischemic stroke. Recently, machine learning has shown a strong ability to classify data and a potential for prediction in the medical field. The combined use of machine learning and the electronic health records of patients could provide clinicians with a more convenient and precise method to identify asymptomatic CAS. Methods Retrospective cohort study using routine clinical data of medical check-up subjects from April 19, 2010 to November 15, 2019. Six machine learning models (logistic regression [LR], random forest [RF], decision tree [DT], eXtreme Gradient Boosting [XGB], Gaussian Naïve Bayes [GNB], and K-Nearest Neighbour [KNN]) were used to predict asymptomatic CAS and compared their predictability in terms of the area under the receiver operating characteristic curve (AUCROC), accuracy (ACC), and F1 score (F1). Results Of the 18,441 subjects, 6553 were diagnosed with asymptomatic CAS. Compared to DT (AUCROC 0.628, ACC 65.4%, and F1 52.5%), the other five models improved prediction: KNN + 7.6% (0.704, 68.8%, and 50.9%, respectively), GNB + 12.5% (0.753, 67.0%, and 46.8%, respectively), XGB + 16.0% (0.788, 73.4%, and 55.7%, respectively), RF + 16.6% (0.794, 74.5%, and 56.8%, respectively) and LR + 18.1% (0.809, 74.7%, and 59.9%, respectively). The highest achieving model, LR predicted 1045/1966 cases (sensitivity 53.2%) and 3088/3566 non-cases (specificity 86.6%). A tenfold cross-validation scheme further verified the predictive ability of the LR. Conclusions Among machine learning models, LR showed optimal performance in predicting asymptomatic CAS. Our findings set the stage for an early automatic alarming system, allowing a more precise allocation of CAS prevention measures to individuals probably to benefit most.
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- 2021
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12. Scaffold-free human mesenchymal stem cell construct geometry regulates long bone regeneration
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Samuel Herberg, Daniel Varghai, Daniel S. Alt, Phuong N. Dang, Honghyun Park, Yuxuan Cheng, Jung-Youn Shin, Anna D. Dikina, Joel D. Boerckel, Marsha W. Rolle, and Eben Alsberg
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Biology (General) ,QH301-705.5 - Abstract
Herberg et al. previously showed functional healing of femoral defects using scaffold-free human mesenchymal stem cell (hMSC) condensates with localized morphogen presentation. In this study, they report the importance of the tubular geometry of MSC condensates in long bone regeneration. Unlike loosely packed hMSC sheets, only hMSC tubes induced regenerate tissue partially resembling normal growth plate.
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- 2021
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13. Establishing a high sensitivity detection method for SARS-CoV-2 IgM/IgG and developing a clinical application of this method
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Chunyan Zhang, Lei Zhou, Hao Liu, Sibing Zhang, Yaping Tian, Junli Huo, Fei Li, Yao Zhang, Bo Wei, Dan Xu, Jinwei Hu, Jiayi Wang, Yuxuan Cheng, Wenjie Shi, Xiuli Xu, Jianping Zhou, Peipei Sang, Xudong Tan, Weiwei Wang, Minjie Zhang, Bin Wang, Yujun Zhou, Kan Zhang, and Kunlun He
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SARS-CoV-2 antibody ,multi-epitopes fusion protein ,time-resolved fluorescence immunoassay ,disease evaluation ,prognosis ,Infectious and parasitic diseases ,RC109-216 ,Microbiology ,QR1-502 - Abstract
ABSTRACTCOVID-19 is caused by SARS-CoV-2 infection and was initially discovered in Wuhan. This outbreak quickly spread all over China and then to more than 20 other countries. SARS-CoV-2 fluorescent microsphere immunochromatographic test strips were prepared by the combination of time-resolved fluorescence immunoassay with a lateral flow assay. The analytical performance and clinical evaluation of this testing method was done and the clinical significance of the testing method was verified. The LLOD of SARS-CoV-2 antibody IgG and IgM was 0.121U/L and 0.366U/L. The specificity of IgM and IgG strips in healthy people and in patients with non-COVID-19 disease was 94%, 96.72% and 95.50%, 99.49%, respectively; and sensitivity of IgM and IgG strips for patients during treatment and follow-up was 63.02%, 37.61% and 87.28%, 90.17%, respectively. The SARS-CoV-2 antibody test strip can provide rapid, flexible and accurate testing, and is able to meet the clinical requirement for rapid on-site testing of virus. The ability to detect IgM and IgG provided a significant benefit for the detection and prediction of clinical course with COVID-19 patients.
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- 2020
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14. SimpleFusion: A Simple Fusion Framework for Infrared and Visible Images.
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Ming Chen, Yuxuan Cheng, Xinwei He, Xinyue Wang, Yan Aze, and Jinhai Xiang
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- 2024
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15. Toward a Team of AI-made Scientists for Scientific Discovery from Gene Expression Data.
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Haoyang Liu, Yijiang Li, Jinglin Jian, Yuxuan Cheng, Jianrong Lu, Shuyi Guo, Jinglei Zhu, Mianchen Zhang, Miantong Zhang, and Haohan Wang
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- 2024
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16. Beyond Pixels: Exploring Human-Readable SVG Generation for Simple Images with Vision Language Models.
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Tong Zhang, Haoyang Liu, Peiyan Zhang, Yuxuan Cheng, and Haohan Wang
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- 2023
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17. ByteGNN: Efficient Graph Neural Network Training at Large Scale.
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Chenguang Zheng, Hongzhi Chen, Yuxuan Cheng, Zhezheng Song, Yifan Wu, Changji Li, James Cheng, Hao Yang, and Shuai Zhang
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- 2022
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18. Decreased Central Macular Choriocapillaris Perfusion Correlates With Increased Low Luminance Visual Acuity Deficits
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Mengxi Shen, Jianqing Li, Yingying Shi, Qinqin Zhang, Ziyu Liu, Hao Zhou, Jie Lu, Yuxuan Cheng, Zhongdi Chu, Xiao Zhou, Jeremy Liu, Xiaoshuang Jiang, Liang Wang, Rita Laiginhas, Luis de Sisternes, Elizabeth A. Vanner, William J. Feuer, Ruikang K. Wang, Giovanni Gregori, and Philip J. Rosenfeld
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Ophthalmology - Published
- 2023
19. Effect and mechanism of nano iron oxide on muskmelon under cadmium stress
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Zhengkang Zou, Yuxuan Cheng, Mengyan Shen, Ying Zhou, Yunqiang Wang, Junli Li, Meifang Qi, and Zhaoyi Dai
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Plant Science - Published
- 2023
20. Biochar and nano-ferric oxide synergistically alleviate cadmium toxicity of muskmelon
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Ying Zhou, Zhengkang Zou, Mengfei Wang, Yunqiang Wang, Junli Li, Lingzhi Qiu, Yuxuan Cheng, and Zhaoyi Dai
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Health, Toxicology and Mutagenesis ,Environmental Chemistry ,General Medicine ,Pollution - Published
- 2023
21. Research on transition corridor boundary of distributed propulsion VTOL fixed wing
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Yuxuan Cheng, Zhou Zhou, and Kelei Wang
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General Engineering - Abstract
The transition state is the most critical and dangerous state of the VTOL fixed wing aircraft in the whole flight process. In this paper, a transition corridor for a distributed propulsion VTOL fixed-wing aircraft is studied based on the lift characteristics of the wing and the power constraints of the power unit. Firstly, according to the sliding flow theory, the dynamic characteristics models of the lift fan system in the front part of the fuselage and the distributed duct system in the rear part of the fuselage were established by introducing the influence factor of the duct, and verified with the test data. Secondly, according to the lift characteristics of the wing, the transition curves of the aircraft at different angles of attack are calculated, in which the transition curves corresponding to the zero-lift attack angle and stall attack angle constitute the lift characteristics transition corridor of the distributed propulsion VTOL fixed-wing aircraft. Finally based on the dynamic performance of the power unit model, calculate the lift characteristic transition each state point in corridor corresponding power demand, according to the power limit of the lift fan system, distributed duct system and power unit total power limitation, get distributed to promote vertical take-off and landing a fixed wing aircraft power limitation in lifting features and power unit under the condition of complete transition corridor. The final results show that the minimum forward velocity is inversely proportional to the attack angle. The power required by the tail distributed duct system will exceed the limit when the aircraft is in low speed and small dip angle transition. For the power limit boundary required, the power limit condition of individual component is stricter than the total power limit condition. The research results of this paper can provide some reference for the transition corridor research of such VTOL fixed-wing aircraft, and on this basis, the subsequent work such as parameter sensitivity analysis and control system design of transition corridor can be carried out.
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- 2022
22. Does the Outer Retinal Thickness Around Geographic Atrophy Represent Another Clinical Biomarker for Predicting Growth?
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Qinqin Zhang, Yingying Shi, Mengxi Shen, Yuxuan Cheng, Hao Zhou, William Feuer, Luis de Sisternes, Giovanni Gregori, Philip J. Rosenfeld, and Ruikang K. Wang
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Ophthalmology ,Geographic Atrophy ,Humans ,Prospective Studies ,Retinal Pigment Epithelium ,Fluorescein Angiography ,Biomarkers ,Tomography, Optical Coherence ,Retrospective Studies - Abstract
To determine whether the outer retinal layer (ORL) thickness around geographic atrophy (GA) could serve as a clinical biomarker to predict the annual enlargement rate (ER) of GA.Retrospective analysis of a prospective, observational case series.Eyes with GA were imaged with a swept-source OCT 6 × 6 mm scan pattern. GA lesions were measured from customized en face OCT images and the annual ERs were calculated. The ORL was defined and segmented from the inner boundary of outer plexiform layer (OPL) to the inner boundary of retinal pigment epithelium (RPE) layer. The ORL thickness was measured at different subregions around GA.A total of 38 eyes from 27 participants were included. The same eyes were used for the choriocapillaris (CC) flow deficit (FD) analysis and the RPE to the Bruch membrane (RPE-BM) distance measurements. A negative correlation was observed between the ORL thickness and the GA growth. The ORL thickness in a 300-μm rim around GA showed the strongest correlation with the GA growth (r = -0.457, P = .004). No correlations were found between the ORL thickness and the CC FDs; however, a significant correlation was found between the ORL thickness and the RPE-BM distances around GA (r = -0.398, P = .013).ORL thickness showed a significant negative correlation with annual GA growth, but also showed a significant correlation with the RPE-BM distances, suggesting that they were dependently correlated with GA growth. This finding suggests that the loss of photoreceptors was associated with the formation of basal laminar deposits around GA.
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- 2022
23. Identification of novel variations in SLC6A8 and GAMT genes causing cerebral creatine deficiency syndrome
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Ming Shen, Guangming Yang, Zhehui Chen, Kai Yang, Hui Dong, Chengliang Yin, Yuxuan Cheng, Chunyan Zhang, Fangyan Gu, Yanling Yang, and Yaping Tian
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Intellectual Disability ,Biochemistry (medical) ,Clinical Biochemistry ,Brain Diseases, Metabolic, Inborn ,Humans ,Guanidinoacetate N-Methyltransferase ,Nerve Tissue Proteins ,Syndrome ,General Medicine ,Child ,Creatine ,Plasma Membrane Neurotransmitter Transport Proteins ,Biochemistry - Abstract
Cerebral creatine deficiency syndromes (CCDSs) are a group of rare mendelian disorders mainly characterized by intellectual disability, movement anomaly, behavior disorder and seizures. SLC6A8, GAMT, and GATM are known genes responsible for CCDS. In this study, seven pediatric patients with developmental delay were recruited and submitted to a series of clinical evaluation, laboratory testing, and genetic analysis. The clinical manifestations and core biochemical indications of each child were basically consistent with the diagnosis of CCDS. Genetic diagnosis determined that all patients were positive for SLC6A8 or GAMT variation. A total of 12 variants were identified in this cohort, including six novel ones. The frequency of these variants, the Revel scores and the conservatism of the affected amino acids support their pathogenicity. Our findings expanded the mutation spectrum of CCDS disorders, and provided solid evidence for the counseling to affected families.
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- 2022
24. Correlation between microalbuminuria and atherosclerotic intracranial and extracranial arterial stenosis in patients with cerebral infarction
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Xiaodong Zhang, Mengying Chen, Qingling Yao, Nan Zhang, Jiaxin Fan, Jinming Shi, Shuang Du, Huiyang Qu, Yuxuan Cheng, Shuyin Ma, Meijuan Zhang, Yizhou Huang, Kaili Shi, and Shuqin Zhan
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Male ,Neurology ,Risk Factors ,Physiology (medical) ,Humans ,Surgery ,Cerebral Infarction ,Constriction, Pathologic ,Neurology (clinical) ,General Medicine ,Atherosclerosis ,Intracranial Arteriosclerosis - Abstract
Microalbuminuria (MAU) reflects the generalized vascular endothelial dysfunction. Whether MAU has correlation with atherosclerotic intracranial and extracranial arterial stenosis in cerebral infarction patients is not known and is explored in the present investigation.We enrolled 255 cerebral infarction patients hospitalized at the department of neurology. All patients underwent digital subtraction angiography (DSA) to evaluate the severity and distribution of intracranial and extracranial arterial stenosis. MAU was expressed as the urine albumin-to-creatinine ratio (UACR). We collected basic information, medical history reviews and laboratory results of each participant. The multivariate logistic regression analysis was utilized to analyze the risk factors for severity and distribution of cerebral arterial stenosis.The prevalence of MAU in patients with cerebral infarction was 39.2%, patients with MAU had older age, lower blood uric acid, higher systolic blood pressure (SBP), higher prevalence of hypertension and diabetes (p 0.05) and higher incidence of atherosclerotic intracranial and extracranial arterial stenosis (χ2 = 5.900, p = 0.015). In multiple logistic regression analysis for intracranial and extracranial arterial stenosis more than 50% or occlusion groups, UACR (OR 1.088 95%CI 1.012-1.170p = 0.022), male (OR 2.196 95%CI 1.085-4.442p = 0.029) as well as SBP (OR 5.870 95%CI 1.026-1.048p = 0.015) showed statistical significance. But UACR had no correlation with the distribution of intracranial and extracranial artery stenosis after adjusting for all potential confounders.Microalbuminuria was an independent risk factor for intracranial and extracranial arterial stenosis more than 50% or occlusion.
- Published
- 2022
25. The relationship between serum cystatin C levels and Hughes motor scale in Guillain-Barré syndrome
- Author
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Mengying Chen, Jinming Shi, Jiaxin Fan, Hong Sun, Qingling Yao, Xiaodong Zhang, Shuang Du, Huiyang Qu, Yuxuan Cheng, Shuyin Ma, Meijuan Zhang, and Shuqin Zhan
- Subjects
Psychiatry and Mental health ,Neurology (clinical) - Published
- 2022
26. Hairpin Structure Facilitates Multiplex High-Fidelity DNA Amplification in Real-Time Polymerase Chain Reaction
- Author
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Kerou Zhang, Alessandro Pinto, Lauren Yuxuan Cheng, Ping Song, Peng Dai, Michael Wang, Luis Rodriguez, Cailin Weller, and David Yu Zhang
- Subjects
Mutation ,DNA ,DNA-Directed DNA Polymerase ,Real-Time Polymerase Chain Reaction ,Multiplex Polymerase Chain Reaction ,DNA Primers ,Analytical Chemistry - Abstract
Clinically and biologically, it is essential to detect rare DNA-sequence variants for early cancer diagnosis or drug-resistance mutation identification. Some of the common quantitative polymerase chain reaction (qPCR)-based variant detection methods are restricted in the limit of detection (LoD) because the DNA polymerases used for these methods have a high polymerase misincorporation rate; thus, the detection sensitivity is sometimes unsatisfactory. With the proofreading activity, high-fidelity (HiFi) DNA polymerases have a 50- to 250-fold higher fidelity. However, there are currently no proper probe-based designs functioning as the fluorescence indicator allowing multiplexed HiFi qPCR reactions, thus restricting the application of HiFi DNA polymerases like the variant detection. We presented the occlusion system, composed of a 5'-overhanged primer with a fluorophore modification and a probe with a short-stem hairpin and a 3' quencher modification. We demonstrated that the occlusion system allowed multiplexing HiFi qPCR reaction, and it was compatible with the current variant-enrichment method to improve the LoD up to 10-fold. Thus, the occlusion system satisfactorily functioned as an efficient fluorescence indicator in HiFi qPCR reactions and allowed the application of HiFi DNA polymerases in variant detection methods to improve detection sensitivity.
- Published
- 2022
27. Investigating the AC079305/DUSP1 Axis as Oxidative Stress-Related Signatures and Immune Infiltration Characteristics in Ischemic Stroke
- Author
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Jiaxin Fan, Shuai Cao, Mengying Chen, Qingling Yao, Xiaodong Zhang, Shuang Du, Huiyang Qu, Yuxuan Cheng, Shuyin Ma, Meijuan Zhang, Yizhou Huang, Nan Zhang, Kaili Shi, and Shuqin Zhan
- Subjects
Aging ,Article Subject ,Cell Biology ,General Medicine ,Biochemistry - Abstract
Background. Oxidative stress (OS) and immune inflammation play complex intersections in the pathophysiology of ischemic stroke (IS). However, a competing endogenous RNA- (ceRNA-) based mechanism linked to the intersections in IS has not been explored. We aimed to identify potential OS-related signatures and analyze immune infiltration characteristics in IS. Methods. Three datasets (GSE22255, GSE110993, and GSE140275) from the GEO database were extracted. Differentially expressed long noncoding RNAs, microRNAs, and messenger RNAs (DElncRNAs, DEmiRNAs, and DEmRNAs) between IS patients and controls were identified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were explored. Moreover, a triple ceRNA network was constructed to reveal transcriptional regulation mechanisms. A comprehensive strategy among least absolute shrinkage and selection operator (LASSO) regression, DEmRNAs, uprelated DEmRNAs, and OS-related genes was adopted to select the best signature. Then, we evaluated and verified the discriminant ability of the signature via receiver operating characteristic (ROC) analysis. Immune infiltration characteristics were explored via the CIBERSORT algorithm. Moreover, the best signature was verified via qPCR and western blot methods in rat brain tissues and PC12 cells. Results. 11 DEmRNAs were identified totally. Enrichment analysis showed that the DEmRNAs were primarily concentrated in MAPK-associated biological processes and immune or inflammation-involved pathways. DUSP1 was identified as the best signature with an area under the ROC curve of 73.5% ( 95 % CI = 57.02 -89.98, sensitivity = 95 % , and specificity = 60 % ) in GSE22255 and 100.0% ( 95 % CI = 100.00 -100.00, sensitivity = 100 % , and specificity = 100 % ) in GSE140275. Importantly, we also identified the AC079305/DUSP1 axis in the ceRNA network. Immune infiltration showed that resting mast cells infiltrate less in IS patients compared with controls. And DUSP1 was negatively correlated with resting mast cells ( r = − 0.703 , P < 0.01 ), whereas it was positively correlated with neutrophils ( r = 0.339 , P < 0.05 ). Both in vivo and in vitro models confirmed the upregulated expression of DUSP1 and the downregulated expression of miR-429. Conclusion. This study identified the ceRNA-based AC079305/DUSP1 axis as a promising OS-related signature for IS. Immune infiltrating cells, especially mast cells, may exert a pivotal role in IS progression. Pharmacological agents targeting signatures, their receptors, or mast cells may shed a novel light on therapeutic targets for IS.
- Published
- 2022
28. Research on deployment process of gravitational airdrop UAV
- Author
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Yuxuan CHENG, Zhou ZHOU, and Zhengping WANG
- Subjects
General Engineering - Abstract
Due to the space limitation of the launching platform, the wings of the space-based gravity delivery UAV need to be folded before launching. In the process of wing folding and launching, the dynamics model of UAV will show the characteristics of multiple rigid bodies and multiple degrees of freedom, and the aerodynamic characteristics of UAV are also quite different from that of cruise stage, so the traditional aircraft dynamics modeling method is no longer applicable. In this paper, the multibody dynamics model of gravitational airdrop UAV is first built based on the Lagrange equation, and then according to the aerodynamic change on unmanned aerial vehicle in deploying process, the angle between the wing and the fuselage is introduced as a new variable, the UAV launch phase nonlinear aerodynamic model is established, and through comparison with software calculation results the reliability of the aerodynamic model is verified. Based on the aerodynamic model and dynamics model, the dynamic response of UAV deployment process is simulated, and the influence of UAV deployment process on UAV subsequent pulling stage under the same control instructions is compared, and the dynamics and kinematics characteristics of gravity launch are studied and explored. Finally, the simulation results are compared with the experimental data, indicating that the multi-body dynamic model established in this paper can accurately describe the dynamic response of UAV in the launching stage and the subsequent modification stage, which can provide reference for the technical personnel engaged in the design, test and use of related models.
- Published
- 2022
29. Automated segmentation and quantification of calcified drusen in 3D swept source OCT imaging
- Author
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Jie Lu, Yuxuan Cheng, Jianqing Li, Ziyu Liu, Mengxi Shen, Qinqin Zhang, Jeremy Liu, Gissel Herrera, Farhan E. Hiya, Rosalyn Morin, Joan Joseph, Giovanni Gregori, Philip J. Rosenfeld, and Ruikang K. Wang
- Subjects
Atomic and Molecular Physics, and Optics ,Article ,Biotechnology - Abstract
Qualitative and quantitative assessments of calcified drusen are clinically important for determining the risk of disease progression in age-related macular degeneration (AMD). This paper reports the development of an automated algorithm to segment and quantify calcified drusen on swept-source optical coherence tomography (SS-OCT) images. The algorithm leverages the higher scattering property of calcified drusen compared with soft drusen. Calcified drusen have a higher optical attenuation coefficient (OAC), which results in a choroidal hypotransmission defect (hypoTD) below the calcified drusen. We show that it is possible to automatically segment calcified drusen from 3D SS-OCT scans by combining the OAC within drusen and the hypoTDs under drusen. We also propose a correction method for the segmentation of the retina pigment epithelium (RPE) overlying calcified drusen by automatically correcting the RPE by an amount of the OAC peak width along each A-line, leading to more accurate segmentation and quantification of drusen in general, and the calcified drusen in particular. A total of 29 eyes with nonexudative AMD and calcified drusen imaged with SS-OCT using the 6 × 6 mm2 scanning pattern were used in this study to test the performance of the proposed automated method. We demonstrated that the method achieved good agreement with the human expert graders in identifying the area of calcified drusen (Dice similarity coefficient: 68.27 ± 11.09%, correlation coefficient of the area measurements: r = 0.9422, the mean bias of the area measurements = 0.04781 mm2).
- Published
- 2023
30. ByteGNN
- Author
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Chenguang Zheng, Hongzhi Chen, Yuxuan Cheng, Zhezheng Song, Yifan Wu, Changji Li, James Cheng, Hao Yang, and Shuai Zhang
- Subjects
General Engineering - Abstract
Graph neural networks (GNNs) have shown excellent performance in a wide range of applications such as recommendation, risk control, and drug discovery. With the increase in the volume of graph data, distributed GNN systems become essential to support efficient GNN training. However, existing distributed GNN training systems suffer from various performance issues including high network communication cost, low CPU utilization, and poor end-to-end performance. In this paper, we propose ByteGNN, which addresses the limitations in existing distributed GNN systems with three key designs: (1) an abstraction of mini-batch graph sampling to support high parallelism, (2) a two-level scheduling strategy to improve resource utilization and to reduce the end-to-end GNN training time, and (3) a graph partitioning algorithm tailored for GNN workloads. Our experiments show that ByteGNN outperforms the state-of-the-art distributed GNN systems with up to 3.5--23.8 times faster end-to-end execution, 2--6 times higher CPU utilization, and around half of the network communication cost.
- Published
- 2022
31. On the Translation of Words and Phrases with Chinese Characteristics after China’s WTO Entry: under the Guidance of Skopos Theory
- Author
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Yuxuan Cheng and Pei Yu
- Published
- 2022
32. High-accurate FE simulation on compressive behavior of steel cruciform column with welding imperfection
- Author
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Yuxuan Cheng, Shuhei Nozawa, and Mikihito Hirohata
- Subjects
Applied Mathematics ,General Engineering ,Computer Graphics and Computer-Aided Design ,Analysis - Published
- 2023
33. Hopper flows of deformable particles
- Author
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Yuxuan Cheng, John D. Treado, Benjamin F. Lonial, Piotr Habdas, Eric R. Weeks, Mark D. Shattuck, and Corey S. O'Hern
- Subjects
Soft Condensed Matter (cond-mat.soft) ,FOS: Physical sciences ,General Chemistry ,Condensed Matter - Soft Condensed Matter ,Condensed Matter Physics - Abstract
Numerous experimental and computational studies show that continuous hopper flows of granular materials obey the Beverloo equation that relates the volume flow rate $Q$ and the orifice width $w$: $Q \sim (w/\sigma_{\rm avg}-k)^{\beta}$, where $\sigma_{\rm avg}$ is the average particle diameter, $k\sigma_{\rm avg}$ is an offset where $Q\sim 0$, the power-law scaling exponent $\beta=d-1/2$, and $d$ is the spatial dimension. Recent studies of hopper flows of deformable particles in different background fluids suggest that the particle stiffness and dissipation mechanism can also strongly affect the power-law scaling exponent $\beta$. We carry out computational studies of hopper flows of deformable particles with both kinetic friction and background fluid dissipation in two and three dimensions. We show that the exponent $\beta$ varies continuously with the ratio of the viscous drag to the kinetic friction coefficient, $\lambda=\zeta/\mu$. $\beta = d-1/2$ in the $\lambda \rightarrow 0$ limit and $d-3/2$ in the $\lambda \rightarrow \infty$ limit, with a midpoint $\lambda_c$ that depends on the hopper opening angle $\theta_w$. We also characterize the spatial structure of the flows and associate changes in spatial structure of the hopper flows to changes in the exponent $\beta$. The offset $k$ increases with particle stiffness until $k \sim k_{\rm max}$ in the hard-particle limit, where $k_{\rm max} \sim 3.5$ is larger for $\lambda \rightarrow \infty$ compared to that for $\lambda \rightarrow 0$. Finally, we show that the simulations of hopper flows of deformable particles in the $\lambda \rightarrow \infty$ limit recapitulate the experimental results for quasi-2D hopper flows of oil droplets in water., Comment: 15 pages, 12 figures
- Published
- 2022
34. An Investigation on Vortex Induced Vibration and Wake Induced Galloping in Tandem Cylinders System
- Author
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Kai Guo, Yuxuan Cheng, Xiantao Fan, Hongsheng Zhang, and Wei Tan
- Abstract
The flow-induced vibration (FIV) of multi cylinders is a problem involving the safety of fluid engineering and energy harvesting. Due to the effect of wake galloping and vortex induced vibration (VIV), the mechanism of two tandem cylinders is more complex than that of a single cylinder. In this study, the vibration modes of two tandem cylinders with different spans (L/D = 1.5–4.0) are investigated at subcritical Reynolds number and high mass damping ratio through wind tunnel tests. In the experiment, the cylinders are free to vibrate in the transverse and in-flow direction. The characteristics of the vibration amplitude and vibration frequency response are discussed with the vibration mode. The results show that the vibration mode is related to the reduced pitches between the cylinders. The vibration of the two tandem cylinder system is combines results of vortex induced vibration and wake induced galloping (WIG). When the span is lower than 2.0, the galloping effect is more obvious than that of larger spans cylinders at the experiment mass damping parameters. The two cylinders turn to vibrate separately as the span grows larger.
- Published
- 2022
35. A MXene/MoS2 heterostructure based biosensor for accurate sweat ascorbic acid detection
- Author
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Yue Zhang, Zheng Wang, Xiaohao Liu, Yating Liu, Yuxuan Cheng, Daxiang Cui, Feng Chen, and Wentao Cao
- Subjects
Materials Chemistry ,Ceramics and Composites ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials - Published
- 2023
36. Decreased Macular Choriocapillaris Perfusion in Eyes With Macular Reticular Pseudodrusen Imaged With Swept-Source OCT Angiography
- Author
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Jianqing Li, Ziyu Liu, Jie Lu, Mengxi Shen, Yuxuan Cheng, Nadia Siddiqui, Hao Zhou, Qinqin Zhang, Jeremy Liu, Gissel Herrera, Farhan E. Hiya, Giovanni Gregori, Ruikang K. Wang, and Philip J. Rosenfeld
- Subjects
General Medicine - Published
- 2023
37. Transcriptome studies on cadmium tolerance and biochar mitigating cadmium stress in muskmelon
- Author
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Yuxuan Cheng, Lingzhi Qiu, Pingkai Shen, Yunqiang Wang, Junli Li, Zhaoyi Dai, Meifang Qi, Ying Zhou, and Zhengkang Zou
- Subjects
Physiology ,Genetics ,Plant Science - Published
- 2023
38. Application of OCT‐Derived Attenuation Coefficient in Acute Burn‐Damaged Skin
- Author
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Jie Lu, Yujiao Zheng, Yuxuan Cheng, Anthony J. Deegan, Teng Liu, Ruikang K. Wang, and Samuel P. Mandell
- Subjects
Burn injury ,genetic structures ,Human skin ,Dermatology ,01 natural sciences ,Burned skin ,010309 optics ,030207 dermatology & venereal diseases ,03 medical and health sciences ,0302 clinical medicine ,Optical coherence tomography ,Dermis ,0103 physical sciences ,Humans ,Medicine ,Skin ,Wound Healing ,integumentary system ,medicine.diagnostic_test ,business.industry ,Skin Injury ,medicine.anatomical_structure ,Attenuation coefficient ,Automatic segmentation ,Surgery ,Epidermis ,Burns ,business ,Tomography, Optical Coherence ,Biomedical engineering - Abstract
BACKGROUND AND OBJECTIVES There remains a need to objectively monitor burn wound healing within a clinical setting, and optical coherence tomography (OCT) is proving itself one of the ideal modalities for just such a use. The aim of this study is to utilize the noninvasive and multipurpose capabilities of OCT, along with its cellular-level resolution, to demonstrate the application of optical attenuation coefficient (OAC), as derived from OCT data, to facilitate the automatic digital segmentation of the epidermis from scan images and to work as an objective indicator for burn wound healing assessment. STUDY DESIGN/MATERIALS AND METHODS A simple, yet efficient, method was used to estimate OAC from OCT images taken over multiple time points following acute burn injury. This method enhanced dermal-epidermal junction (DEJ) contrast, which facilitated the automatic segmentation of the epidermis for subsequent thickness measurements. In addition, we also measured and compared the average OAC of the dermis within said burns for correlative purposes. RESULTS Compared with unaltered OCT maps, enhanced DEJ contrast was shown in OAC maps, both from single A-lines and completed B-frames. En face epidermal thickness and dermal OAC maps both demonstrated significant changes between imaging sessions following burn injury, such as a loss of epidermal texture and decreased OAC. Quantitative analysis also showed that OAC of acute burned skin decreased below that of healthy skin following injury. CONCLUSIONS Our study has demonstrated that the OAC estimated from OCT data can be used to enhance imaging contrast to facilitate the automatic segmentation of the epidermal layer, as well as help elucidate our understanding of the pathological changes that occur in human skin when exposed to acute burn injury, which could serve as an objective indicator of skin injury and healing.
- Published
- 2021
39. Cost-Efficient Sequence-Based Nonextensible Oligonucleotide in Real-Time PCR and High-Throughput Sequencing
- Author
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Kerou Zhang, Ping Song, Peng Dai, Jinny Xuemeng Zhang, Lucia Ruojia Wu, Lauren Yuxuan Cheng, Alessandro Pinto, Lawrence Kwong, Karina Cabrera, Ruoxin Wen, and David Yu Zhang
- Subjects
Fluid Flow and Transfer Processes ,Process Chemistry and Technology ,Mutation ,Oligonucleotides ,High-Throughput Nucleotide Sequencing ,Bioengineering ,Real-Time Polymerase Chain Reaction ,Instrumentation ,Sensitivity and Specificity - Abstract
Molecular detection of disease-associated mutations, especially those with low abundance, is essential for academic research and clinical diagnosis. Certain variant detection methods reach satisfactory sensitivity and specificity in detecting rare mutations based on the introduction of blocking oligos to prevent the amplification of wild-type or unwanted templates, thus selectively amplifying and enriching the mutations. These blocking oligos usually suppress PCR amplification through the 3' chemical modifications, with high price, slow synthesis, and reduced purity. Herein, we introduce chemistry-free designs to block enzymatic extension during PCR by the steric hindrance from the secondary structures attached to the 3' end of the oligos (nonextensible oligonucleotide, NEO). We demonstrated that NEO efficiently prohibited the extension of both Taq and high-fidelity DNA polymerases. By further applying NEO as blockers in blocker displacement amplification (BDA) qPCR, multiplex BDA (mBDA) NGS, and quantitative BDA (QBDA) NGS methods, we showed that NEO blockers had performance comparable with previously validated chemical modifications. Comparison experiments using QBDA with NEO blockers and droplet digital PCR (ddPCR) on clinical formalin-fixed paraffin-embedded (FFPE) samples exhibited 100% concordance. Lastly, the ability of NEO to adjust plex uniformity through changes of PCR amplification efficiency was demonstrated in an 80-plex NGS panel.
- Published
- 2022
40. Non-invasive assessment of diameter-dependent cutaneous vascular alterations with age using optical coherence tomography angiography
- Author
-
Takuma Hoshino, Yusuke Hara, Masato Ninomiya, Toyonobu Yamashita, Chika Katagiri, Motoki Oguri, Masako Katsuyama, Yuandong J. Li, Yuxuan Cheng, Nhan M. Le, and Ruikang Wang
- Published
- 2022
41. A Meta-Analysis of Blinatumomab Bridging Transplantation in Patients with Refractory/Relapsed Acute Lymphoblastic Leukemia: Safety and Efficacy Outcomes
- Author
-
Wan Zhang, Yuxuan Cheng, Jing Liu, and Aijun Zhang
- Subjects
History ,Polymers and Plastics ,Business and International Management ,Industrial and Manufacturing Engineering - Published
- 2022
42. Insights to the Transition Regimes of Flow-Induced Vibration for Three Tandem Cylinders
- Author
-
Kai Guo, Yuxuan Cheng, Xiantao Fan, Yang Wang, Wei Tan, and Hongsheng Zhang
- Published
- 2022
43. Investigating the
- Author
-
Jiaxin, Fan, Shuai, Cao, Mengying, Chen, Qingling, Yao, Xiaodong, Zhang, Shuang, Du, Huiyang, Qu, Yuxuan, Cheng, Shuyin, Ma, Meijuan, Zhang, Yizhou, Huang, Nan, Zhang, Kaili, Shi, and Shuqin, Zhan
- Subjects
Gene Expression Regulation, Neoplastic ,Inflammation ,MicroRNAs ,Oxidative Stress ,Animals ,Humans ,Dual Specificity Phosphatase 1 ,Gene Regulatory Networks ,RNA, Long Noncoding ,Ischemic Stroke ,Rats - Abstract
Oxidative stress (OS) and immune inflammation play complex intersections in the pathophysiology of ischemic stroke (IS). However, a competing endogenous RNA- (ceRNA-) based mechanism linked to the intersections in IS has not been explored. We aimed to identify potential OS-related signatures and analyze immune infiltration characteristics in IS.Three datasets (GSE22255, GSE110993, and GSE140275) from the GEO database were extracted. Differentially expressed long noncoding RNAs, microRNAs, and messenger RNAs (DElncRNAs, DEmiRNAs, and DEmRNAs) between IS patients and controls were identified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were explored. Moreover, a triple ceRNA network was constructed to reveal transcriptional regulation mechanisms. A comprehensive strategy among least absolute shrinkage and selection operator (LASSO) regression, DEmRNAs, uprelated DEmRNAs, and OS-related genes was adopted to select the best signature. Then, we evaluated and verified the discriminant ability of the signature via receiver operating characteristic (ROC) analysis. Immune infiltration characteristics were explored via the CIBERSORT algorithm. Moreover, the best signature was verified via qPCR and western blot methods in rat brain tissues and PC12 cells.11 DEmRNAs were identified totally. Enrichment analysis showed that the DEmRNAs were primarily concentrated in MAPK-associated biological processes and immune or inflammation-involved pathways.This study identified the ceRNA-based
- Published
- 2021
44. Be careful of Collet-Sicard syndrome: A rare result of carotid artery dissection
- Author
-
Kaili Shi, Nan Zhang, Yanling Li, Hong Sun, Yizhou Huang, Meijuan Zhang, Shuyin Ma, Shuang Du, Yuxuan Cheng, Huiyang Qu, and Shuqin Zhan
- Subjects
Carotid Artery Diseases ,Carotid Arteries ,Neurology ,Humans ,Neurology (clinical) ,Hypoglossal Nerve Diseases ,Cranial Nerve Diseases - Published
- 2021
45. Single-Tube qPCR Detection and Quantitation of Hotspot Mutations Down to 0.01% Variant Allele Fraction
- Author
-
Kerou Zhang, Luis Rodriguez, Lauren Yuxuan Cheng, Michael Wang, and David Yu Zhang
- Subjects
Mutation ,Leukocytes, Mononuclear ,High-Throughput Nucleotide Sequencing ,Real-Time Polymerase Chain Reaction ,Alleles ,Analytical Chemistry - Abstract
Clinically and biologically, rare DNA sequence variants are significant and informative. However, existing common detection technologies are either complex and time-consuming in workflow, or restricted in the limit of detection (LoD), or do not allow for multiplexing. Blocker displacement amplification (BDA) method can stably and effectively detect and enrich multiple rare variants with LoD around 0.1% variant allele fraction (VAF). Nonetheless, the detailed mutation information has to be identified by additional sequencing technologies. Here, we present allele-specific BDA (As-BDA), a method combining BDA with allele-specific TaqMan (As-TaqMan) probes for effective variant enrichment and simultaneous single nucleotide variant or small insertions and deletions (INDELs) profiling. We demonstrated that As-BDA could detect mutations down to 0.01% VAF. Further, As-BDA could detect up to four mutations with low to 0.1% VAF per reaction using only 15 ng DNA input. The median error of As-BDA in VAF determination is approximately 9.1%. Comparison experiments using As-BDA and droplet digital PCR on peripheral blood mononuclear cell clinical samples showed 100% concordance for samples with mutations at ≥ 0.1% VAF. Hence, we have shown that As-BDA can achieve simultaneous enrichment and identification of multiple targeted mutations within the same reaction with high clinical sensitivity and specificity, thus helpful for clinical diagnosis.
- Published
- 2021
46. Automatic geographic atrophy segmentation using optical attenuation in OCT scans with deep learning
- Author
-
Zhongdi Chu, Liang Wang, Xiao Zhou, Yingying Shi, Yuxuan Cheng, Rita Laiginhas, Hao Zhou, Mengxi Shen, Qinqin Zhang, Luis de Sisternes, Aaron Y. Lee, Giovanni Gregori, Philip J. Rosenfeld, and Ruikang K. Wang
- Subjects
genetic structures ,sense organs ,Atomic and Molecular Physics, and Optics ,eye diseases ,Article ,Biotechnology - Abstract
A deep learning algorithm was developed to automatically identify, segment, and quantify geographic atrophy (GA) based on optical attenuation coefficients (OACs) calculated from optical coherence tomography (OCT) datasets. Normal eyes and eyes with GA secondary to age-related macular degeneration were imaged with swept-source OCT using 6 × 6 mm scanning patterns. OACs calculated from OCT scans were used to generate customized composite en face OAC images. GA lesions were identified and measured using customized en face sub-retinal pigment epithelium (subRPE) OCT images. Two deep learning models with the same U-Net architecture were trained using OAC images and subRPE OCT images. Model performance was evaluated using DICE similarity coefficients (DSCs). The GA areas were calculated and compared with manual segmentations using Pearson’s correlation and Bland-Altman plots. In total, 80 GA eyes and 60 normal eyes were included in this study, out of which, 16 GA eyes and 12 normal eyes were used to test the models. Both models identified GA with 100% sensitivity and specificity on the subject level. With the GA eyes, the model trained with OAC images achieved significantly higher DSCs, stronger correlation to manual results and smaller mean bias than the model trained with subRPE OCT images (0.940 ± 0.032 vs 0.889 ± 0.056, p = 0.03, paired t-test, r = 0.995 vs r = 0.959, mean bias = 0.011 mm vs mean bias = 0.117 mm). In summary, the proposed deep learning model using composite OAC images effectively and accurately identified, segmented, and quantified GA using OCT scans.
- Published
- 2021
47. Hairpin structure facilitates multiplex high-fidelity DNA amplification in real-time PCR
- Author
-
David Zhang, Luis L. Rodriguez, Alessandro Pinto, Ping Song, Peng Dai, Lauren Yuxuan Cheng, Michael Wang, Kerou Zhang, and Cailin Weller
- Subjects
Early cancer ,Real-time polymerase chain reaction ,biology ,DNA polymerase ,Chemistry ,biology.protein ,Multiplex ,Computational biology ,Primer (molecular biology) ,Dna amplification ,Polymerase ,DNA sequencing - Abstract
Effective polymerase chain reactions (PCR) are important in bio-laboratories. It is essential to detect rare DNA-sequence variants for early cancer diagnosis or for drug-resistance mutations identification. Some of the common detection quantitative PCR (qPCR) methods are restricted in the limit of detection (LoD) because of the high polymerase misincorporation rate in Taq DNA polymerases. High-fidelity (HiFi) DNA polymerases have a 50- to 250-fold higher fidelity. Yet, there are currently no proper designs for multiplexed HiFi qPCR reactions. Moreover, the popularity of targeting highly multiplex DNA sequences requires minimizing PCR side products, as the potential of dimerization grows quadratically as the plexes of primers increases. Efforts tried before were either an add-on step, or technology-specific, or requiring high-level computing skills. There lacks an easy-to-apply and cost-effective method for dimerization reduction. Here, we presented the Occlusion System, composed of a 59-overhanged primer and a probe with a short-stem hairpin. We demonstrated that it allowed multiplexing high-fidelity qPCR reaction, it was also compatible with the current variant-enrichment method to improve the LoD by 10-fold. Further, we found that the Occlusion System reduced the dimerization up to 10-fold in highly multiplexed PCR. Thus, the Occlusion System satisfactorily improved both qPCR sensitivity and PCR efficiency.
- Published
- 2021
48. Calibration-free NGS quantitation of mutations below 0.01% VAF
- Author
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Pengying Hao, Michael Xiangjiang Wang, Sherry Xi Chen, Weijie Yao, Jinny X. Zhang, David Zhang, Ghayas C. Issa, Jabra Zarka, Lucia Ruojia Wu, Lauren Yuxuan Cheng, Lawrence N. Kwong, and Peng Dai
- Subjects
Neoplasm, Residual ,Science ,General Physics and Astronomy ,Computational biology ,Biology ,medicine.disease_cause ,General Biochemistry, Genetics and Molecular Biology ,Deep sequencing ,Article ,medicine ,Humans ,In patient ,Indel ,Gene ,Melanoma ,Mutation ,Multidisciplinary ,Myeloid leukemia ,High-Throughput Nucleotide Sequencing ,General Chemistry ,Minimal residual disease ,Leukemia, Myeloid, Acute ,Calibration ,Next-generation sequencing ,Calibration free - Abstract
Quantitation of rare somatic mutations is essential for basic research and translational clinical applications including minimal residual disease (MRD) detection. Though unique molecular identifier (UMI) has suppressed errors for rare mutation detection, the sequencing depth requirement is high. Here, we present Quantitative Blocker Displacement Amplification (QBDA) which integrates sequence-selective variant enrichment into UMI quantitation for accurate quantitation of mutations below 0.01% VAF at only 23,000X depth. Using a panel of 20 genes recurrently altered in acute myeloid leukemia, we demonstrate quantitation of various mutations including single base substitutions and indels down to 0.001% VAF at a single locus with less than 4 million sequencing reads, allowing sensitive MRD detection in patients during complete remission. In a pan-cancer panel and a melanoma hotspot panel, we detect mutations down to 0.1% VAF using only 1 million reads. QBDA provides a convenient and versatile method for sensitive mutation quantitation using low-depth sequencing., Quantification of rare somatic mutations is essential for basic research and translational applications. Here the authors present Quantitative Blocker Displacement Amplification allowing for accurate detection of mutations below 0.01% VAF.
- Published
- 2021
49. Direct capture and sequencing reveal ultra-short single-stranded DNA in biofluids
- Author
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Lucia Ruojia Wu, Lauren Yuxuan Cheng, David Zhang, and Peng Dai
- Subjects
Biomarker ,chemistry.chemical_compound ,education.field_of_study ,chemistry ,Population ,Computational biology ,education ,DNA extraction ,DNA - Abstract
Direct capture and sequencing revealed a new DNA population in biofluids, named ultra-short single-stranded DNA (ussDNA), which was neglected by conventional DNA extraction and sequencing approaches. Evaluation of the size distribution and abundance of ussDNA in biofluids manifested generality of its presence in human, animal, and plants. Red blood cells were found to contain abundant ussDNA with enriched functional elements, and thus possesses great potential as a novel DNA biomarker.
- Published
- 2021
50. Single Tube qPCR detection and quantitation of hotspot mutations down to 0.01% VAF
- Author
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Lauren Yuxuan Cheng, Luis L. Rodriguez, Kerou Zhang, and David Zhang
- Subjects
Detection limit ,Mutation ,Biology ,medicine.disease_cause ,Molecular biology ,DNA sequencing ,Single tube ,chemistry.chemical_compound ,chemistry ,Clinical diagnosis ,medicine ,TaqMan ,Digital polymerase chain reaction ,DNA - Abstract
Clinically and biologically, rare DNA sequence variants are significant and informative. However, existing detection technologies are either complex in workflow, or restricted in the limit of detection (LoD), or do not allow for multiplexing. Blocker displacement amplification (BDA) method can stably and effectively detect and enrich multiple rare variants with LoD around 0.1% variant allele fraction (VAF). Nonetheless, the detailed mutation information has to be identified by additional sequencing technologies. Here, we present allele-specific BDA (As-BDA), a method combining BDA with allele-specific TaqMan (As-TaqMan) probes for effective variant enrichment and simultaneous SNV profiling. We demonstrated that As-BDA could detect mutations down to 0.01% VAF. Further, As-BDA could detect up to four mutations with low to 0.1% VAF per reaction using only 15 ng DNA input. The median error of As-BDA in VAF determination is approximately 9.1%. Comparison experiments using As-BDA and droplet digital PCR (ddPCR) on peripheral blood mononuclear cell (PBMC) clinical samples showed 100% concordance for samples with mutations at ≥ 0.1% VAF. Hence, we have shown that As-BDA can achieve simultaneous enrichment and identification of multiple targeted mutations within the same reaction with high clinical sensitivity and specificity, thus helpful for clinical diagnosis.
- Published
- 2021
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