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"Zhao, Lin"
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Mapping the epigenetic modifications of DNA and RNA
Over 17 and 160 types of chemical modifications have been identified in DNA and RNA, respectively. The interest in understanding the various biological functions of DNA and RNA modifications has lead to the cutting-edged fields of epigenomics and epitranscriptomics. Developing chemical and biological tools to detect specific modifications in the genome or transcriptome has greatly facilitated their study. Here, we review the recent technological advances in this rapidly evolving field. We focus on high-throughput detection methods and biological findings for these modifications, and discuss questions to be addressed as well. We also summarize third-generation sequencing methods, which enable long-read and single-molecule sequencing of DNA and RNA modification.
Journal Article
Contextual Region-Based Convolutional Neural Network with Multilayer Fusion for SAR Ship Detection
Synthetic aperture radar (SAR) ship detection has been playing an increasingly essential role in marine monitoring in recent years. The lack of detailed information about ships in wide swath SAR imagery poses difficulty for traditional methods in exploring effective features for ship discrimination. Being capable of feature representation, deep neural networks have achieved dramatic progress in object detection recently. However, most of them suffer from the missing detection of small-sized targets, which means that few of them are able to be employed directly in SAR ship detection tasks. This paper discloses an elaborately designed deep hierarchical network, namely a contextual region-based convolutional neural network with multilayer fusion, for SAR ship detection, which is composed of a region proposal network (RPN) with high network resolution and an object detection network with contextual features. Instead of using low-resolution feature maps from a single layer for proposal generation in a RPN, the proposed method employs an intermediate layer combined with a downscaled shallow layer and an up-sampled deep layer to produce region proposals. In the object detection network, the region proposals are projected onto multiple layers with region of interest (ROI) pooling to extract the corresponding ROI features and contextual features around the ROI. After normalization and rescaling, they are subsequently concatenated into an integrated feature vector for final outputs. The proposed framework fuses the deep semantic and shallow high-resolution features, improving the detection performance for small-sized ships. The additional contextual features provide complementary information for classification and help to rule out false alarms. Experiments based on the Sentinel-1 dataset, which contains twenty-seven SAR images with 7986 labeled ships, verify that the proposed method achieves an excellent performance in SAR ship detection.
Journal Article
The Effects of Dietary Nutrition on Sleep and Sleep Disorders
Sleep disorder significantly affects the life quality of a large number of people but is still an underrecognized disease. Dietary nutrition is believed to play a significant impact on sleeping wellness. Many nutritional supplements have been used trying to benefit sleep wellness. However, the relationship between nutritional components and sleep is complicated. Nutritional factors vary dramatically with different diet patterns and depend significantly on the digestive and metabiotic functions of each individual. Moreover, nutrition can profoundly affect the hormones and inflammation status which directly or indirectly contribute to insomnia. In this review, we summarized the role of major nutritional factors, carbohydrates, lipids, amino acids, and vitamins on sleep and sleep disorders and discussed the potential mechanisms.
Journal Article
Targeted protein degradation: mechanisms, strategies and application
Traditional drug discovery mainly focuses on direct regulation of protein activity. The development and application of protein activity modulators, particularly inhibitors, has been the mainstream in drug development. In recent years, PROteolysis TArgeting Chimeras (PROTAC) technology has emerged as one of the most promising approaches to remove specific disease-associated proteins by exploiting cells’ own destruction machinery. In addition to PROTAC, many different targeted protein degradation (TPD) strategies including, but not limited to, molecular glue, Lysosome-Targeting Chimaera (LYTAC), and Antibody-based PROTAC (AbTAC), are emerging. These technologies have not only greatly expanded the scope of TPD, but also provided fresh insights into drug discovery. Here, we summarize recent advances of major TPD technologies, discuss their potential applications, and hope to provide a prime for both biologists and chemists who are interested in this vibrant field.
Journal Article
Application of Berberine on Treating Type 2 Diabetes Mellitus
Traditional Chinese medicine (TCM) performs a good clinical practice and is showing a bright future in the treatment of diabetes mellitus (DM). TCM treatment has certain advantages of less toxicity and/or side effects, and herbs could provide multiple therapeutic effects. Berberine (BBR) is a classical natural medicine. In this review, we summarize the application of BBR in the treatment of DM from two aspects. First, modern pharmacological effects of BBR on glucose metabolism are summarized, such as improving insulin resistance, promoting insulin secretion, inhibiting gluconeogenesis in liver, stimulating glycolysis in peripheral tissue cells, modulating gut microbiota, reducing intestinal absorption of glucose, and regulating lipid metabolism. BBR is used to treat diabetic nephropathy (DPN), diabetic neuropathy (DN), and diabetic cardiomyopathy due to its antioxidant and anti-inflammatory activities. Second, the clinical application of BBR is reviewed, such as listing some clinical trials on the effectiveness and safety of BBR, explaining applicable stage and syndrome, the reasonable dose and dose formulation, and the toxicity and/or side effects. This review provides scientific evidence about BBR, as well as introducing some traditional Chinese medical theory and clinical experience, in order to guide clinician to use BBR more suitably and reasonably.
Journal Article
Insulin resistance assessed by estimated glucose disposal rate and risk of incident cardiovascular diseases among individuals without diabetes: findings from a nationwide, population based, prospective cohort study
Background
Recent studies have suggested that insulin resistance (IR) contributes to the development of cardiovascular diseases (CVD), and the estimated glucose disposal rate (eGDR) is considered to be a reliable surrogate marker of IR. However, most existing evidence stems from studies involving diabetic patients, potentially overstating the effects of eGDR on CVD. Therefore, the primary objective of this study is to examine the relationship of eGDR with incidence of CVD in non-diabetic participants.
Method
The current analysis included individuals from the China Health and Retirement Longitudinal Study (CHARLS) who were free of CVD and diabetes mellitus but had complete data on eGDR at baseline. The formula for calculating eGDR was as follows: eGDR (mg/kg/min) = 21.158 − (0.09 × WC) − (3.407 × hypertension) − (0.551 × HbA1c) [WC (cm), hypertension (yes = 1/no = 0), and HbA1c (%)]. The individuals were categorized into four subgroups according to the quartiles (Q) of eGDR. Crude incidence rate and hazard ratios (HRs) with 95% confidence intervals (CIs) were computed to investigate the association between eGDR and incident CVD, with the lowest quartile of eGDR (indicating the highest grade of insulin resistance) serving as the reference. Additionally, the multivariate adjusted restricted cubic spine (RCS) was employed to examine the dose–response relationship.
Results
We included 5512 participants in this study, with a mean age of 58.2 ± 8.8 years, and 54.1% were female. Over a median follow-up duration of 79.4 months, 1213 incident CVD cases, including 927 heart disease and 391 stroke, were recorded. The RCS curves demonstrated a significant and linear relationship between eGDR and all outcomes (all
P
for non-linearity > 0.05). After multivariate adjustment, the lower eGDR levels were founded to be significantly associated with a higher risk of CVD. Compared with participants with Q1 of eGDR, the HRs (95% CIs) for those with Q2 − 4 were 0.88 (0.76 − 1.02), 0.69 (0.58 − 0.82), and 0.66 (0.56 − 0.79). When assessed as a continuous variable, per 1.0-SD increase in eGDR was associated a 17% (HR: 0.83, 95% CI: 0.78 − 0.89) lower risk of CVD, with the subgroup analyses indicating that smoking status modified the association (
P
for interaction = 0.012). Moreover, the mediation analysis revealed that obesity partly mediated the association. Additionally, incorporating eGDR into the basic model considerably improve the predictive ability for CVD.
Conclusion
A lower level of eGDR was found to be associated with increased risk of incident CVD among non-diabetic participants. This suggests that eGDR may serve as a promising and preferable predictor and intervention target for CVD.
Journal Article
Role of inflammation, immunity, and oxidative stress in hypertension: New insights and potential therapeutic targets
Hypertension is regarded as the most prominent risk factor for cardiovascular diseases, which have become a primary cause of death, and recent research has demonstrated that chronic inflammation is involved in the pathogenesis of hypertension. Both innate and adaptive immunity are now known to promote the elevation of blood pressure by triggering vascular inflammation and microvascular remodeling. For example, as an important part of innate immune system, classically activated macrophages (M1), neutrophils, and dendritic cells contribute to hypertension by secreting inflammatory cy3tokines. In particular, interferon-gamma (IFN-γ) and interleukin-17 (IL-17) produced by activated T lymphocytes contribute to hypertension by inducing oxidative stress injury and endothelial dysfunction. However, the regulatory T cells and alternatively activated macrophages (M2) may have a protective role in hypertension. Although inflammation is related to hypertension, the exact mechanisms are complex and unclear. The present review aims to reveal the roles of inflammation, immunity, and oxidative stress in the initiation and evolution of hypertension. We envisage that the review will strengthen public understanding of the pathophysiological mechanisms of hypertension and may provide new insights and potential therapeutic strategies for hypertension.
Journal Article
The hypoxia-driven crosstalk between tumor and tumor-associated macrophages: mechanisms and clinical treatment strategies
Given that hypoxia is a persistent physiological feature of many different solid tumors and a key driver for cancer malignancy, it is thought to be a major target in cancer treatment recently. Tumor-associated macrophages (TAMs) are the most abundant immune cells in the tumor microenvironment (TME), which have a large impact on tumor development and immunotherapy. TAMs massively accumulate within hypoxic tumor regions. TAMs and hypoxia represent a deadly combination because hypoxia has been suggested to induce a pro-tumorigenic macrophage phenotype. Hypoxia not only directly affects macrophage polarization, but it also has an indirect effect by altering the communication between tumor cells and macrophages. For example, hypoxia can influence the expression of chemokines and exosomes, both of which have profound impacts on the recipient cells. Recently, it has been demonstrated that the intricate interaction between cancer cells and TAMs in the hypoxic TME is relevant to poor prognosis and increased tumor malignancy. However, there are no comprehensive literature reviews on the molecular mechanisms underlying the hypoxia-mediated communication between tumor cells and TAMs. Therefore, this review has the aim to collect all recently available data on this topic and provide insights for developing novel therapeutic strategies for reducing the effects of hypoxia.
Journal Article
The micro(nano)plastics perspective: exploring cancer development and therapy
Microplastics, as an emerging environmental pollutant, have received widespread attention for their potential impact on ecosystems and human health. Microplastics are defined as plastic particles less than 5 millimeters in diameter and can be categorized as primary and secondary microplastics. Primary microplastics usually originate directly from industrial production, while secondary microplastics are formed by the degradation of larger plastic items. Microplastics are capable of triggering cytotoxicity and chronic inflammation, and may promote cancer through mechanisms such as pro-inflammatory responses, oxidative stress and endocrine disruption. In addition, improved microplastics bring new perspectives to cancer therapy, and studies of microplastics as drug carriers are underway, showing potential for high targeting and bioavailability. Although current studies suggest an association between microplastics and certain cancers (e.g., lung, liver, and breast cancers), the long-term effects and specific mechanisms still need to be studied. This review aimed at exploring the carcinogenicity of microplastics and their promising applications in cancer therapy provides important directions for future research and emphasizes the need for multidisciplinary collaboration to address this global health challenge.
Journal Article