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"Lu, Yuwen"
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A novel early diagnostic framework for chronic diseases with class imbalance
2022
Chronic diseases are one of the most severe health issues in the world, due to their terrible clinical presentations such as long onset cycle, insidious symptoms, and various complications. Recently, machine learning has become a promising technique to assist the early diagnosis of chronic diseases. However, existing works ignore the problems of feature hiding and imbalanced class distribution in chronic disease datasets. In this paper, we present a universal and efficient diagnostic framework to alleviate the above two problems for diagnosing chronic diseases timely and accurately. Specifically, we first propose a network-limited polynomial neural network (NLPNN) algorithm to efficiently capture
high-level
features hidden in chronic disease datasets, which is data augmentation in terms of its feature space and can also avoid over-fitting. Then, to alleviate the class imbalance problem, we further propose an attention-empowered NLPNN algorithm to improve the diagnostic accuracy for sick cases, which is also data augmentation in terms of its sample space. We evaluate the proposed framework on nine public and two real chronic disease datasets (partly with class imbalance). Extensive experiment results demonstrate that the proposed diagnostic algorithms outperform state-of-the-art machine learning algorithms, and can achieve superior performances in terms of accuracy, recall, F1, and G_mean. The proposed framework can help to diagnose chronic diseases timely and accurately at an early stage.
Journal Article
G2Basy: A framework to improve the RNN language model and ease overfitting problem
2021
Recurrent neural networks are efficient ways of training language models, and various RNN networks have been proposed to improve performance. However, with the increase of network scales, the overfitting problem becomes more urgent. In this paper, we propose a framework—G2Basy—to speed up the training process and ease the overfitting problem. Instead of using predefined hyperparameters, we devise a gradient increasing and decreasing technique that changes the parameters training batch size and input dropout simultaneously by a user-defined step size. Together with a pretrained word embedding initialization procedure and the introduction of different optimizers at different learning rates, our framework speeds up the training process dramatically and improves performance compared with a benchmark model of the same scale. For the word embedding initialization, we propose the concept of “artificial features” to describe the characteristics of the obtained word embeddings. We experiment on two of the most often used corpora—the Penn Treebank and WikiText-2 datasets—and both outperform the benchmark results and show potential towards further improvement. Furthermore, our framework shows better results with the larger and more complicated WikiText-2 corpus than with the Penn Treebank. Compared with other state-of-the-art results, we achieve comparable results with network scales hundreds of times smaller and within fewer training epochs.
Journal Article
Research on the Thermal Conductivity and Microstructure of Calcium Lignosulfonate-Magnesium Oxide Solidified Loess
2025
Loess, characterized by high porosity, a loose structure, and weak cementation, is highly prone to deformation and cracking under thermal stress, which significantly affects the bearing capacity of foundations and the stability of underground engineering structures. This study introduces an innovative approach that utilizes the eco-friendly modifier calcium lignosulfonate (CL) in combination with magnesium oxide (MgO) for the carbonation solidification treatment of loess. The research systematically investigated the thermal conductivity and underlying micro-mechanisms of the treated soil. A series of tests, including analyses of basic physical properties, measurements of thermal conductivity, X-ray diffraction (XRD), and scanning electron microscopy (SEM), were conducted to evaluate the effects of CL dosage, freeze–thaw cycles, moisture content, and dry density on the thermal conductivity of carbonation-solidified loess. The results indicate that carbonated solidified loess absorbed approximately 6% of CO2, while effectively reducing its collapsibility grade to a slightly collapsible classification. Additionally, its thermal conductivity decreased by 16.7%, thereby mitigating the influence of various environmental factors. Based on the experimental results, a microscopic mechanism model was developed. This study presents a sustainable and innovative technical solution for stabilizing loess foundations in cold regions.
Journal Article
Urinary Exosomal miRNAs as biomarkers of bladder Cancer and experimental verification of mechanism of miR-93-5p in bladder Cancer
2021
Background
Bladder cancer (BC) is one of the most common malignancies globally. Early diagnosis of it can significantly improve patients’ survival and quality of life. Urinary exosomes (UEs)-derived miRNAs might be a promising biomarker for BC detection.
Method
A total of 12 patients with BC and 4 non-cancerous participants (as healthy control) were recruited from a single center between March 2018 and December 2019 as the discovery set. Midstream urine samples from each participants were collected and high-throughput sequencing and differentially expression analysis were conducted. Combined with miRNA expression profile of BC tissue from The Cancer Genome Atlas (TCGA), miRNAs biomarkers for BC were determined. Candidate miRNAs as biomarkers were selected followed by verification with a quantitative reverse-transcription polymerase chain reaction assay in an independent validation cohort consisting of 53 BC patients and 51 healthy controls. The receiver-operating characteristic (ROC) curve was established to evaluate the diagnostic performance of UE-derived miRNAs. The possible mechanism of miRNAs were revealed by bioinformatic analysis and explored in vitro experiments.
Results
We identified that miR-93-5p, miR-516a-5p were simultaneously significantly increased both in UEs from BC compared with healthy control and BC tissue compared with normal tissue, which were verified by RT-qPCR in the validation cohort. Subsequently, the performance to discover BC of the miR-93-5p, miR-516a-5p was further verified with an area under ROC curve (AUC) of 0.838 and 0.790, respectively, which was significantly higher than that of urine cytology (AUC = 0.630). Moreover, miR-93-5p was significantly increased in muscle-invasive BC compared with non-muscle-invasive BC with an AUC of 0.769. Bioinformatic analysis revealed that B-cell translocation gene 2(BTG2) gene may be the hub target gene of miR-93-5p. In vitro experiments verified that miR-93-5p suppressed BTG2 expression and promoted BC cells proliferation, invasion and migration.
Conclusion
Urine derived exosomes have a distinct miRNA profile in BC patients, and urinary exosomal miRNAs could be used as a promising non-invasive tool to detect BC. In vitro experiments suggested that miR-93-5p overexpression may contribute to BC progression via suppressing BTG2 expression.
Journal Article
Multi-objective optimization approach of shelter location with maximum equity: an empirical study in Xin Jiekou district of Nanjing, China
by
Chen, Wei
,
Lu, Yuwen
,
Zhai, Guofang
in
Algorithms
,
Application programming interface
,
Construction costs
2023
Based on the inadequacies and neglect of the equity of refuge resources, refuge demands and the evacuation allocation of traditional methodologies, this study put forwards the multi-objectives layout optimization model of shelters which firstly realizes the maximum equity of shelter location. Our approach has the objectives of maximizing equity, minimizing overall egress time and minimizing the quantity of new shelters. The high-precision population is established through mobile signaling data, while the optimization model adopts a circular circulatory allocation rule derived from a gravity model. The shorter the evacuation time, the larger the shelter capacity and thus more refugees are allocated to the shelter. The evacuation time is determined by the application programming interface (API) of the Baidu Map open platform with Python, which exhibits the authentic evacuation paths and real-time traffic conditions. This study designs a three-stage algorithm 'genetic algorithm-exhaustive method-evaluation'. The first process of algorithm calculates the minimum quantity of new shelters; the second process selects the feasible layout schemes and determines Pareto optimum solutions; and the third stage evaluates the Pareto optimum solution based on the shelter construction cost and the accessibility from shelters to emergency supply storage points to determine the best location scheme. This study regards Xin Jiekou district in Nanjing as a case area to demonstrate reliability and availability of the proposed methodology.
Journal Article
Epicardial transplantation of antioxidant polyurethane scaffold based human amniotic epithelial stem cell patch for myocardial infarction treatment
Myocardial infarction (MI) is a leading cause of death globally. Stem cell therapy is considered a potential strategy for MI treatment. Transplantation of classic stem cells including embryonic, induced pluripotent and cardiac stem cells exhibited certain repairing effect on MI via supplementing cardiomyocytes, however, their clinical applications were blocked by problems of cell survival, differentiation, functional activity and also biosafety and ethical concerns. Here, we introduced human amniotic epithelial stem cells (hAESCs) featured with immunomodulatory activities, immune-privilege and biosafety, for constructing a stem cell cardiac patch based on porous antioxidant polyurethane (PUR), which demonstrated decent hAESCs compatibility. In rats, the administration of PUR-hAESC patch significantly reduced fibrosis and facilitated vascularization in myocardium after MI and consequently improved cardiac remodeling and function. Mechanistically, the patch provides a beneficial microenvironment for cardiac repair by facilitating a desirable immune response, paracrine modulation and limited oxidative milieu. Our findings may provide a potential therapeutic strategy for MI.
Myocardial infarction is a leading cause of death globally. Stem cell therapy is considered a potential treatment. Here, the authors propose an antioxidant polyurethane-based cardiac patch with stem cells that provides antioxidation, immune remodeling and paracrine modulation for myocardial repair.
Journal Article
Effectiveness of 308-nm Excimer Light with Pimecrolimus and Crisaborole in Pediatric Vitiligo: A Retrospective Study
2026
To systematically evaluate the efficacy and safety of 308-nm excimer light therapy combined with topical pimecrolimus cream and crisaborole ointment in children with non-segmental vitiligo, using dermatoscopy, ImageJ software, Wood's lamp examination, and a color difference meter.
A retrospective study was conducted involving 120 pediatric patients diagnosed with non-segmental vitiligo who attended the Department of Dermatology, The Second Affiliated Hospital of Wenzhou Medical University, between January 2023 and December 2023. Patients were divided into three groups based on treatment regimen. Group 1 received 308-nm excimer light therapy combined with pimecrolimus cream. Group 2 received 308-nm excimer light therapy combined with crisaborole ointment. Control group received 308-nm excimer light therapy. Baseline images of skin lesions were obtained under natural light, Wood's lamp illumination, and dermatoscopic examination. All patients received once-weekly phototherapy sessions for 12 consecutive weeks, with treatment efficacy assessed at 4-week intervals. Treatment response rates, adverse events, and repigmentation patterns were systematically evaluated and compared across treatment groups.
The overall treatment efficacy and repigmentation area demonstrated a progressive increase with successive treatment cycles. After 4 weeks of therapy, the response rates for Group 1, Group 2, and the control group were 34.1%, 32.1%, and 23.8%, respectively, with no statistically significant difference observed (P > 0.05). After 8 weeks of treatment, the response rates increased to 63.4%, 60.2%, and 42.8%, respectively, with statistically significant differences among groups (P < 0.05). Following 12 weeks of treatment, the response rates for Group 1, Group 2, and the control group further increased to 76.8%, 71.7%, and 54.8%, respectively (P < 0.05). The combination therapy groups exhibited significantly higher efficacy rates compared with the phototherapy-only group. Clinical efficacy varied significantly across different anatomical sites (P < 0.05), with the highest treatment response observed in the face and neck, followed by the trunk, extremities, and acral regions. Regarding treatment safety, no statistically significant differences in the incidence of adverse reactions were observed between the combination therapy groups and the phototherapy-only group (P > 0.05).
With increasing treatment duration, the therapeutic efficacy and repigmentation area of vitiligo lesions show a progressive improvement. The combination of 308-nm excimer light therapy with topical pimecrolimus cream and crisaborole ointment demonstrates favorable efficacy in pediatric vitiligo, with only mild and well-tolerated adverse reactions. The integrated use of dermatoscopy, ImageJ software, Wood's lamp examination, and a color difference meter provides an objective, quantitative, and reproducible approach for digitally documenting changes in lesion color and area before and after vitiligo treatment.
Journal Article
A biodegradable, flexible photonic patch for in vivo phototherapy
2023
Diagnostic and therapeutic illumination on internal organs and tissues with high controllability and adaptability in terms of spectrum, area, depth, and intensity remains a major challenge. Here, we present a flexible, biodegradable photonic device called iCarP with a micrometer scale air gap between a refractive polyester patch and the embedded removable tapered optical fiber. ICarP combines the advantages of light diffraction by the tapered optical fiber, dual refractions in the air gap, and reflection inside the patch to obtain a bulb-like illumination, guiding light towards target tissue. We show that iCarP achieves large area, high intensity, wide spectrum, continuous or pulsatile, deeply penetrating illumination without puncturing the target tissues and demonstrate that it supports phototherapies with different photosensitizers. We find that the photonic device is compatible with thoracoscopy-based minimally invasive implantation onto beating hearts. These initial results show that iCarP could be a safe, precise and widely applicable device suitable for internal organs and tissue illumination and associated diagnosis and therapy.
Illuminating internal organs and tissues with high controllability and adaptability remains challenging. Here the authors present a flexible, biodegradable photonic device called iCarP for large area, high intensity, wide spectrum, deeply penetrating, continuous or pulsatile illumination.
Journal Article
eIF4A, a target of siRNA derived from rice stripe virus, negatively regulates antiviral autophagy by interacting with ATG5 in Nicotiana benthamiana
2021
Autophagy is induced by viral infection and has antiviral functions in plants, but the underlying mechanism is poorly understood. We previously identified a viral small interfering RNA (vsiRNA) derived from rice stripe virus (RSV) RNA4 that contributes to the leaf-twisting and stunting symptoms caused by this virus by targeting the host eukaryotic translation initiation factor 4A (eIF4A) mRNA for silencing. In addition, autophagy plays antiviral roles by degrading RSV p3 protein, a suppressor of RNA silencing. Here, we demonstrate that eIF4A acts as a negative regulator of autophagy in Nicotiana benthamiana . Silencing of Nb eIF4A activated autophagy and inhibited RSV infection by facilitating autophagic degradation of p3. Further analysis showed that Nb eIF4A interacts with Nb ATG5 and interferes with its interaction with ATG12. Overexpression of Nb eIF4A suppressed Nb ATG5-activated autophagy. Moreover, expression of vsiRNA-4A, which targets Nb eIF4A mRNA for cleavage, induced autophagy by silencing Nb eIF4A . Finally, we demonstrate that eIF4A from rice, the natural host of RSV, also interacts with Os ATG5 and suppresses Os ATG5-activated autophagy, pointing to the conserved function of eIF4A as a negative regulator of antiviral autophagy. Taken together, these results reveal that eIF4A negatively regulates antiviral autophagy by interacting with ATG5 and that its mRNA is recognized by a virus-derived siRNA, resulting in its silencing, which induces autophagy against viral infection.
Journal Article
Ubiquitin-Like protein 5 interacts with the silencing suppressor p3 of rice stripe virus and mediates its degradation through the 26S proteasome pathway
by
Lu, Yuwen
,
Rao, Shaofei
,
Li, Junmin
in
Amino acids
,
Biodegradation
,
Biology and Life Sciences
2020
Ubiquitin like protein 5 (UBL5) interacts with other proteins to regulate their function but differs from ubiquitin and other UBLs because it does not form covalent conjugates. Ubiquitin and most UBLs mediate the degradation of target proteins through the 26S proteasome but it is not known if UBL5 can also do that. Here we found that the UBL5s of rice and Nicotiana benthamiana interacted with rice stripe virus (RSV) p3 protein. Silencing of NbUBL5s in N. benthamiana facilitated RSV infection, while UBL5 overexpression conferred resistance to RSV in both N. benthamiana and rice. Further analysis showed that NbUBL5.1 impaired the function of p3 as a suppressor of silencing by degrading it through the 26S proteasome. NbUBL5.1 and OsUBL5 interacted with RPN10 and RPN13, the receptors of ubiquitin in the 26S proteasome. Furthermore, silencing of NbRPN10 or NbRPN13 compromised the degradation of p3 mediated by NbUBL5.1. Together, the results suggest that UBL5 mediates the degradation of RSV p3 protein through the 26S proteasome, a previously unreported plant defense strategy against RSV infection.
Journal Article