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"Li, Qian"
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scTour: a deep learning architecture for robust inference and accurate prediction of cellular dynamics
Despite the continued efforts, a batch-insensitive tool that can both infer and predict the developmental dynamics using single-cell genomics is lacking. Here, I present scTour, a novel deep learning architecture to perform robust inference and accurate prediction of cellular dynamics with minimal influence from batch effects. For inference, scTour simultaneously estimates the developmental pseudotime, delineates the vector field, and maps the transcriptomic latent space under a single, integrated framework. For prediction, scTour precisely reconstructs the underlying dynamics of unseen cellular states or a new independent dataset. scTour’s functionalities are demonstrated in a variety of biological processes from 19 datasets.
Journal Article
Optimizing short video strategies for intelligent communication in university campus culture construction using circular intuitionistic fuzzy COCOFISO modeling
Short-video communication is becoming a more common tool in universities to influence campus culture, but the choice of strategies and tools is not a straightforward one due to the variety of goals at particular institutions, limited resources, and the lack of reliability in expert advice. The paper proposes a circular intuitionistic fuzzy combined compromise solution to the ideal solution optimization (C-IF COCOFISO) method for ranking candidate short-video strategies based on a number of possibly conflicting criteria. Modelling the expert judgments as circular intuitionistic fuzzy constructions, which are combined and their aggregation is performed in a manner incorporating a combined compromise solution to ideal solution optimization (COCOFISO) procedure, led to consistently stable and easily interpretable priority scores. The criteria include the suitability of cultural relevance, effectiveness in communication, flexibility in technology, opportunities for student engagement, ethics, and sustainability. The framework consolidates fuzzy expressed fuzzy modelling and a clear-cut compromise-driven ranking pipeline, enabling decision-makers to handle waffling and trade-offs in one process. In particular, it combines C-IF data with COCOFISO to overcome competing goals and incomplete decisions, offers a step-by-step procedure that produces reproducible weights and rankings that are appropriate to institutional planning, and is tested on an actual university case, including sensitivity and cross-method comparisons. The findings show that C-IF COCOFISO provides a similar ranking and is more sensitive to cultural goals than the minimal requirements of decision-making processes, making it a flexible and convenient tool for drawing short-video communication plans in higher education.
Journal Article
Evaluation of high performance concrete hardness properties using fuzzy logic based modeling
For construction engineering to be most effective, it’s essential to understand the hardness properties of high-performance concrete (HPC), such as compressive strength and slump. However, predicting these properties is challenging due to complex, non-linear relationships and the inherent variability of factors like the water-cement ratio and mineral additives. Traditional modeling methods often struggle to handle these uncertainties effectively. This paper introduces a novel Hybrid Fuzzy Artificial Neural Network (HFANN) architecture that integrates fuzzy logic with advanced machine learning models, including Support Vector Regression (SVR), Multilayer Perceptron (MLP), and Gradient Boosting Machine (GBM), all optimized by the Chaos Game Optimization (CGO). The fuzzy logic system employs Gaussian membership functions and a Sugeno-type rule base to preprocess inputs, generating 18 fuzzy features per sample to capture data uncertainties. The CGO enhances model performance by optimizing hyperparameters and ensemble weights through a chaotic search based on the Sierpinski triangle. The HFANN framework demonstrates superior predictive accuracy compared to traditional models. It achieves a 25% reduction in RMSE for compressive strength and R² values of 0.98 for compressive strength and 0.97–0.99 for slump across training, validation, and testing phases. These results, validated through MANOVA and Tukey’s HSD tests, indicate significant improvements over conventional methods. The HFANN framework offers a robust tool for enhancing HPC mix design and advancing sustainable construction practices.
Journal Article
Direct cell reprogramming: approaches, mechanisms and progress
The reprogramming of somatic cells with defined factors, which converts cells from one lineage into cells of another, has greatly reshaped our traditional views on cell identity and cell fate determination. Direct reprogramming (also known as transdifferentiation) refers to cell fate conversion without transitioning through an intermediary pluripotent state. Given that the number of cell types that can be generated by direct reprogramming is rapidly increasing, it has become a promising strategy to produce functional cells for therapeutic purposes. This Review discusses the evolution of direct reprogramming from a transcription factor-based method to a small-molecule-driven approach, the recent progress in enhancing reprogrammed cell maturation, and the challenges associated with in vivo direct reprogramming for translational applications. It also describes our current understanding of the molecular mechanisms underlying direct reprogramming, including the role of transcription factors, epigenetic modifications, non-coding RNAs, and the function of metabolic reprogramming, and highlights novel insights gained from single-cell omics studies.Direct reprogramming converts cells from one lineage into cells of another without going through an intermediary pluripotent state. This Review describes our current understanding of the molecular mechanisms underlying direct reprogramming as well as the progress in improving its efficiency and the maturation of reprogrammed cells, and the challenges associated with its translational applications.
Journal Article
Clinical application of liquid biopsy in colorectal cancer: detection, prediction, and treatment monitoring
Colorectal cancer (CRC) is one of the most prevalent malignancies affecting the gastrointestinal tract and is ranked third among cancers with the highest incidence and second-highest mortality rate worldwide. CRC exhibits a slow progression providing a wide treatment window. The currently employed CRC screening methods have shown great potential to prevent CRC and reduce CRC-related morbidity and mortality. The diagnosis of CRC is achieved by colonoscopy and tissue biopsy, with studies showing that liquid biopsy is more effective in detecting and diagnosing early CRC patients. Increasing number of studies have shown that the tumor components shed into circulating blood can be detected in liquid form, and can be applied in the clinical management of CRC. Analysis of circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), or tumor-associated platelets (TEPs) in the blood can be used for early screening and diagnosis of CRC, aid tumor staging, treatment response monitoring, and prediction of CRC recurrence and metastasis in a minimally invasive manner. This chapter provides an updated review of CTCs, ctDNA, and TEPs as novel biomarkers for CRC, highlighting their strengths and limitations.
Journal Article
The circular RNA ACR attenuates myocardial ischemia/reperfusion injury by suppressing autophagy via modulation of the Pink1/ FAM65B pathway
Dysregulated autophagy is associated with many pathological disorders such as cardiovascular diseases. Emerging evidence has suggested that circular RNAs (circRNAs) have important roles in some biological processes. However, it remains unclear whether circRNAs participate in the regulation of autophagy. Here we report that a circRNA, termed autophagy-related circular RNA (ACR), represses autophagy and myocardial infarction by targeting Pink1-mediated phosphorylation of FAM65B. ACR attenuates autophagy and cell death in cardiomyocytes. Moreover, ACR protects the heart from ischemia/reperfusion (I/R) injury and reduces myocardial infarct sizes. We identify Pink1 as an ACR target to mediate the function of ACR in cardiomyocyte autophagy. ACR activates Pink1 expression through directly binding to Dnmt3B and blocking Dnmt3B-mediated DNA methylation of Pink1 promoter. Pink1 suppresses autophagy and Pink1 transgenic mice show reduced myocardial infarction sizes. Further, we find that FAM65B is a downstream target of Pink1 and Pink1 phosphorylates FAM65B at serine 46. Phosphorylated FAM65B inhibits autophagy and cell death in the heart. Our findings reveal a novel role for the circRNA in regulating autophagy and ACR-Pink1-FAM65B axis as a regulator of autophagy in the heart will be potential therapeutic targets in treatment of cardiovascular diseases.
Journal Article
Parental beliefs and the influence of formal and informal literacy environments on preschoolers’ attitudes toward English learning
English learning among Chinese preschoolers has increased in recent years. Despite policies that strongly oppose external English instruction for this age group, many parents are unrelenting and persist in providing English learning opportunities for their children. This study seeks to address how formal and informal literacy activities within the Home Literacy Environment (HLE) mediate the relationship between parental beliefs and Chinese children’s attitudes towards learning English in a foreign language context. Specifically, it explores: (1) how formal literacy activities within the HLE mediate this relationship, (2) how informal literacy activities within the HLE mediate this relationship. The study involved 405 participants who completed a questionnaire on family demographics, beliefs about the importance of early English education, the HLE, and children’s attitudes towards English learning. Quantitative data were analyzed using Structural Equation Modeling (SEM) with a Partial Least Squares (PLS) approach. Parental beliefs positively influence children’s attitudes towards English through formal and informal learning. These results highlight the importance of fostering a supportive and engaging HLE to enhance children’s positive attitudes towards learning English. The implications suggest that policy and practice should recognize the value of various literacy activities in early childhood education, particularly in the context of a foreign language and academically focused Asian society.
Journal Article
Exercise training modalities in patients with type 2 diabetes mellitus: a systematic review and network meta-analysis
Introduction
Current international guidelines recommend aerobic, resistance, and combined exercises for the management of type 2 diabetes mellitus (T2DM). In our study, we conducted a network meta-analysis to assess the comparative impact of different exercise training modalities on glycemic control, cardiovascular risk factors, and weight loss in patients with T2DM.
Methods
We searched five electronic databases to identify randomized controlled trials (RCTs) that compared the differences between different exercise training modalities for patients with T2DM. The risk of bias in the included RCTs was evaluated according to the Cochrane tool. Network meta-analysis was performed to calculate mean difference the ratio of the mean and absolute risk differences. Data were analyzed using R-3.4.0.
Results
A total of 37 studies with 2208 patients with T2DM were included in our study. Both supervised aerobic and supervised resistance exercises showed a significant reduction in HbA1c compared to no exercise (0.30% lower, 0.30% lower, respectively), however, there was a less reduction when compared to combined exercise (0.17% higher, 0.23% higher). Supervised aerobic also presented more significant improvement than no exercise in fasting plasma glucose (9.38 mg/dl lower), total cholesterol (20.24 mg/dl lower), triacylglycerol (19.34 mg/dl lower), and low-density lipoprotein cholesterol (11.88 mg/dl lower). Supervised resistance showed more benefit than no exercise in improving systolic blood pressure (3.90 mmHg lower]) and total cholesterol (22.08 mg/dl lower]. In addition, supervised aerobic exercise was more powerful in improving HbA1c and weight loss than unsupervised aerobic (HbA1c: 0.60% lower; weight loss: 5.02 kg lower) and unsupervised resistance (HbA1c: 0.53% lower) exercises.
Conclusion
Compared with either supervised aerobic or supervised resistance exercise alone, combined exercise showed more pronounced improvement in HbA1c levels; however, there was a less marked improvement in some cardiovascular risk factors. In terms of weight loss, there were no significant differences among the combined, supervised aerobic, and supervised resistance exercises.
Trial registration
Our study protocol was registered with the International Prospective Register of Systematic Reviews (PROSPERO); registration number:
CRD42017067518
.
Journal Article