Publications by authors named "Wanlu Liu"

Article Synopsis
  • * A benchmark study was conducted using experimental single-cell immune profiling datasets, highlighting that the methods TRUST4 and MiXCR provided superior performance in TCR reconstruction, while DeRR also showed notable accuracy.
  • * The introduction of the YASIM-scTCR simulator allows for the generation of diverse TCR-derived sequences, but the study found that sequencing depth significantly affects the success of TCR construction from scRNA-seq data.
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  • The study explores the relationship between pulmonary toxicity from polycyclic aromatic hydrocarbons (PAHs) and the potential modifying role of vitamin D, specifically in the context of early signs of chronic obstructive pulmonary disease (COPD).
  • Using data from the NHANES 2007-2012, the researchers analyzed how PAHs negatively impact lung function and how vitamin D levels could counteract these effects among participants, particularly those with early lung dysfunction.
  • Results indicate that higher vitamin D levels are associated with better lung function and lower risk of early lung dysfunction, suggesting that vitamin D may mediate some negative impacts of PAHs through metabolic mechanisms.
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CD8 T cells exhibit remarkable phenotypic diversity in inflammation and cancer. However, a comprehensive understanding of their clonal landscape and dynamics remains elusive. Here we introduce scAtlasVAE, a deep-learning-based model for the integration of large-scale single-cell RNA sequencing data and cross-atlas comparisons.

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Background: Elevated homocysteine (Hcy) levels have been linked to cardiovascular disease (CVD), but their association with cardiometabolic multimorbidity (CMM) remains uncertain.

Methods: Data from the baseline survey of the China Northwest Cohort-Ningxia Project (CNC-NX) were used to recruit 22,566 participants. Demographic characteristics, lifestyle factors, and laboratory exam results were collected.

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The small intestine contains a two-front nutrient supply environment created by luminal dietary and microbial metabolites (enteral side) and systemic metabolites from the host (serosal side). Yet, it is unknown how each side contributes differentially to the small intestinal physiology. Here, we generated a comprehensive, high-resolution map of the small intestinal two-front nutrient supply environment.

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Fluorescent porous materials based on aggregation-induced emission (AIE) are growing into a sparkling frontier in biomedical applications. Exploring those materials represents a win-win integration and has recently progressed at a rapid pace, mainly benefiting from intrinsic advantages including tunable pore size and structure, strong guest molecule encapsulation ability, superior biocompatibility, and photophysical outcomes. With the great significance and rapid progress in this area, this review provides an integrated picture on AIE luminogen-based porous materials.

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The rapid advancement of cell therapies underscores the importance of understanding fundamental cellular attributes. Among these, cell fitness-how transplanted cells adapt to new microenvironments and maintain functional stability in vivo-is crucial. This study identifies a chemical compound, FPH2, that enhances the fitness of human chondrocytes and the repair of articular cartilage, which is typically nonregenerative.

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Article Synopsis
  • - The study investigates how inflammatory (DII) and antioxidant (CDAI) dietary patterns relate to early signs of Chronic Obstructive Pulmonary Disease (COPD) and how metabolic disorders might influence these associations, using data from over 9,500 individuals in a national health survey.
  • - Results show a higher DII correlates with worse lung function and increased metabolic issues, while a higher CDAI is linked to better lung function and fewer metabolic problems, suggesting that the dietary antioxidant intake can mitigate the negative impacts of an inflammatory diet.
  • - The analysis reveals that metabolic indicators like Triglyceride-glucose index (TyG) play a role in mediating the relationships between these dietary patterns and lung function outcomes
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Hyperuricemia (HUA), or elevated uric acid in the blood, has become more prevalent in recent years. Polyphenols, which are known to have good inhibitory activity on xanthine oxidoreductase (XOR), are effective in uric acid reduction. In this review, we address the structure-activity relationship of flavonoids that inhibit XOR activity from two perspectives: the key residues of XOR and the structural properties of flavonoids.

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The incidence of Alzheimer's disease (AD) is rising globally, yet its treatment and prediction of this condition remain challenging due to the complex pathophysiological mechanisms associated with it. Consequently, the objective of the present study was to analyze and characterize the molecular mechanisms underlying ferroptosis‑related genes (FEGs) in the pathogenesis of AD, as well as to construct a prognostic model. The findings will provide new insights for the future diagnosis and treatment of AD.

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In droplet-based single-cell and single-nucleus RNA-seq assays, systematic contamination of ambient RNA molecules biases the quantification of gene expression levels. Existing methods correct the contamination for all genes globally. However, there lacks specific evaluation of correction efficacy for varying contamination levels.

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  • Calcium homeostasis imbalance can lead to chronic diseases, making effective calcium supplements crucial for health.
  • The study focused on identifying peptide calcium chelates from soybean peptides to enhance calcium absorption while minimizing side effects.
  • Two specific peptides (GGDLVS and YEGVIL) were found to exhibit high calcium binding capacity, and the research aimed to clarify how the amino acid positions influence this binding efficiency.
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The advancement of Long-Read Sequencing (LRS) techniques has significantly increased the length of sequencing to several kilobases, thereby facilitating the identification of alternative splicing events and isoform expressions. Recently, numerous computational tools for isoform detection using long-read sequencing data have been developed. Nevertheless, there remains a deficiency in comparative studies that systemically evaluate the performance of these tools, which are implemented with different algorithms, under various simulations that encompass potential influencing factors.

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Background: Juvenile Idiopathic Arthritis (JIA) is a condition that occurs when individuals under the age of 16 develop arthritis that lasts for more than six weeks, and the cause is unknown. The development of JIA may be linked to serum metabolites. Nevertheless, the association between JIA pathogenesis and serum metabolites is unclear, and there are discrepancies in the findings across studies.

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Objectives: Frailty is an age-related syndrome associated with poor health outcomes. Studies in developed countries indicate that the dietary inflammatory index (DII) and dietary total antioxidant capacity (DTAC) are important dietary factors influencing the risk of frailty in older adults. However, few studies have explored the association between DII, DTAC, and frailty among older Chinese adults.

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  • The study investigates congenital vertebral malformation, which affects about 0.13-0.50 per 1000 live births, focusing on its complex genetic causes using data from 873 affected individuals and 3794 controls.
  • Findings reveal that 12.0% of the cases have identifiable genetic causes, with a specific emphasis on muscle-related disease mechanisms.
  • Gene tests highlight key risk genes associated with significant effects, indicating their importance during various developmental stages of the spine, enhancing our understanding of spinal development and associated malformations.
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Background: The CRISPR/Cas systems have emerged as powerful tools in genome engineering. Recent studies highlighting the crucial role of transposable elements (TEs) have stimulated research interest in manipulating these elements to understand their functions. However, designing single guide RNAs (sgRNAs) that are specific and efficient for TE manipulation is a significant challenge, given their sequence repetitiveness and high copy numbers.

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The most prevalent and insidious type of kidney cancer is kidney clear cell carcinoma (KIRC). Thioredoxin-interacting protein () encodes a thioredoxin-binding protein involved in cellular energy metabolism, redox homeostasis, apoptosis induction and inflammatory responses. However, the relationship between , immune infiltration and its prognostic value in KIRC remains unclear.

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The occupational groups exposed to air pollutants, particularly PM2.5, are closely linked to the initiation and advancement of respiratory disorders. The aim of this study is to investigate the potential protective properties of selenium-enriched soybean peptides (Se-SPeps), a novel Se supplement, in mitigating apoptosis triggered by PM2.

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Food-derived oligopeptides (FOPs) exhibit various bioactivities. However, little was known about their sequence changes in the gastrointestinal tract and the effect of changes on bioactivities. FOPs' sequence features, changes and effects on bioactivities have been summarised.

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Background: Adiposity and insulin resistance (IR) are closely associated with hypertension; however, the role of interactions between obesity phenotypes and IR in hypertension is unclear. This study aimed to evaluate the interactions of body mass index (BMI), waist circumference (WC), and body fat percentage (BF%) with IR on hypertension risk.

Methods: We analyzed data from 4888 participants (mean age 57 years, 41.

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Background: The triglyceride glucose-body mass index (TyG-BMI) is a surrogate indicator of insulin resistance. However, the association of TyG-BMI with heart failure (HF) in individuals with diabetes mellitus or prediabetes mellitus is unknown.

Methods: This study included 7,472 participants aged 20-80 years old with prediabetes or diabetes from the National Health and Nutrition Examination Survey (2007-2018).

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Article Synopsis
  • Atherosclerosis is a serious health problem that can cause heart diseases, and current treatments have some side effects.
  • Flavonoids, which are natural compounds found in fruits and vegetables, may be safer and help protect the heart better than existing drugs.
  • Research shows that flavonoids can reduce harmful substances in the blood and improve good substances, helping to lower inflammation and support heart health.
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Background: Fetal skeletal dysplasia is a diverse group of degenerative diseases of bone and cartilage disorders that can lead to movement disorder and even death. This study aims to evaluate the diagnostic yield of sonographic examination and genetic testing for fetal skeletal dysplasia.

Methods: From September 2015 to April 2021, the study investigated 24 cases with suspected short-limb fetuses, which were obtained from Tongji Hospital affiliated to Tongji Medical College of Huazhong University of Science and Technology.

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The severity of global flood disasters is growing, causing loss of human life and property. Building a high-resilience social system, an important means of sustainable flood control, can address these flood-related issues. Numerous studies have carried out disaster resilience evaluations and explored the correlation between flood disaster loss and intensity, but neglected to analyze the role of resilience construction in disaster loss reduction.

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