iResNetDM: An interpretable deep learning approach for four types of DNA methylation modification prediction.

Motivation: Although several computational methods for predicting DNA methylation modifications have been developed, two main limitations persist: 1) All of the models are currently confined to binary predictors, which merely determine the presence or absence of DNA methylation modifications and thus prevent comprehensive analyses of the interrelations among varied modification types. Multi-class classification models for RNA modifications have been developed, and a comparable approach for DNA is essential. 2) Few previous studies offer adequate explanations of how models make decisions, instead relying on the extraction and visualization of attention matrices, which have identified few motifs and do not provide sufficient insights into the model decision-making process.

[Spatiotemporal Variation and Influencing Factors of Atmospheric Aerosol in the Middle Region of the Yarlung Zangbo River Basin from 2000 to 2020].

Based on the aerosol optical depth （AOD） of the MODIS MCD19A2 dataset from 2000 to 2020, combined with meteorological data, land use/land cover data, and socio-economic data, the spatiotemporal distribution of AOD in the middle region of the Yarlung Zangbo River Basin was analyzed using STL and Theil-Sen Median trend estimation and the influence of natural and anthropogenic factors on AOD was revealed using GeoDetector, XGBoost model and SHAP analysis. The results showed that the spatial heterogeneity of AOD in the middle region of the Yarlung Zangbo River Basin was obvious, which was mainly controlled by topography, with high AOD value concentrated in the valley with the altitude lower than 4 300 m. Owing to the precipitation and surface wind speed, the seasonal difference of AOD was obvious, with the highest in winter.

A Supramolecular Protein Assembly Intrinsically Rescues Memory Deficits in an Alzheimer's Disease Mouse Model.

Supramolecular protein assemblies have been used as intelligent drug delivery systems that can encapsulate drugs and transport them to specific tissues or cells. However, the known methods for designing supramolecular protein assemblies for transportation across the blood-brain barrier (BBB) remain challenging and inefficient. Herein, we report that the supramolecular recombinant-protein-based strategy enables the biosynthesis and production of a supramolecular protein assembly that is intrinsically capable of crossing the BBB.

A genetic study to identify pathogenic mechanisms and drug targets for benign prostatic hyperplasia: a multi-omics Mendelian randomization study.

Benign prostatic hyperplasia (BPH) as a common geriatric disease in urology, the incidence and prevalence are rapidly increasing with the aging society, prompting an urgent need for effective prevention and treatment of BPH. However, limited therapeutic efficacy and higher risk of complications result in the treatment of BPH remaining challenging. The unclear pathogenic mechanism also hampers further exploration of therapeutic approaches for BPH.

Monomeric C-reactive protein is associated with severity and prognosis of decompensated hepatitis B cirrhosis.

C-reactive protein (CRP) is an acute-phase protein produced by the liver in response to infection and during chronic inflammatory disorders. Systemic inflammation is a major driver of cirrhosis progression from the compensated to the decompensated stage. Previous studies have shown that pentameric CRP (pCRP) to be a weak predictor of disease severity and prognosis in patients with decompensated hepatitis B cirrhosis, with it being only helpful for identifying patients with a higher short-term risk of death under certain conditions.

Exploring the mechanism of 6-Methoxydihydrosanguinarine in the treatment of lung adenocarcinoma based on network pharmacology, molecular docking and experimental investigation.

Background: 6-Methoxydihydrosanguinarine (6-MDS) has shown promising potential in fighting against a variety of malignancies. Yet, its anti‑lung adenocarcinoma (LUAD) effect and the underlying mechanism remain largely unexplored. This study sought to explore the targets and the probable mechanism of 6-MDS in LUAD through network pharmacology and experimental validation.

A feature optimization study based on a diabetes risk questionnaire.

Introduction: The prevalence of diabetes, a common chronic disease, has shown a gradual increase, posing substantial burdens on both society and individuals. In order to enhance the effectiveness of diabetes risk prediction questionnaires, optimize the selection of characteristic variables, and raise awareness of diabetes risk among residents, this study utilizes survey data obtained from the risk factor monitoring system of the Centers for Disease Control and Prevention in the United States.

Methods: Following univariate analysis and meticulous screening, a more refined dataset was constructed.

Diabetes prediction model for unbalanced community follow-up data set based on optimal feature selection and scorecard.

Objectives: Diabetes is a metabolic disease and early detection is crucial to ensuring a healthy life for people with prediabetes. Community care plays an important role in public health, but the association between community follow-up of key life characteristics and diabetes risk remains unclear. Based on the method of optimal feature selection and risk scorecard, follow-up data of diabetes patients are modeled to assess diabetes risk.

Bioinformatics Prediction and Experimental Validation of the Role of Macrophage Polarization and Ferroptosis in Gestational Diabetes Mellitus.

Purpose: Gestational diabetes mellitus (GDM) is a common metabolic disorder during pregnancy that is associated with placental inflammation and adverse pregnancy outcomes. However, the mechanisms of inflammation in GDM are still unclear.

Methods: Bulk transcriptome, single-cell transcriptome, clinical information, and samples were collected from GSE154414, GSE70493, GSE173193 and a retrospective cohort.

Functional characterization of four mono-terpene synthases (TPSs) provided insight into the biosynthesis of volatile monoterpenes in the medicinal herb .

Unlabelled: , a wooden plant belonging to the family Asteraceae, is a medicinal herb with anticancer, antiviral, and multiple pharmacological effects, which are believed to be caused by its essential oil. The essential oil from is comprised of mono- and sesqui-terpenes as the majority. Unfortunately, this plant has been facing the challenge of resource shortage, which could be effectively alleviated by biological engineering.

Genome-wide analyzation and functional characterization on the TPS family provide insight into the biosynthesis of mono-terpenes in the camphor tree.

Terpene synthase (TPS) plays an important role in terpenoids biosynthesis. Cinnamomum camphora (camphor tree) contains dozens of terpenoids with medicinal value, especially borneol, which has been widely used since ancient times. However, limited information is available regarding the genome-wide identification and characterization of the TPS family in the C.

Identification and Validation a Necroptosis-Related Prognostic Signature in Cervical Cancer.

Necroptosis is a promising novel target for cervical cancer therapy. Nevertheless, differentially expressed necroptosis-related genes (NRGs) in cervical cancer and their associations with prognosis are far from fully clarified. In this study, differentially expressed NRGs (DE-NRGs) were screened out and their bio-function was elucidated.

The association between urinary organophosphate insecticide metabolites and erectile dysfunction in the United States.

Organophosphate (OP) insecticides are the main chemicals used in agriculture for pest elimination, and they have been linked with many diseases. However, there is no literature regarding the impacts of organophosphate insecticide metabolite exposure on erectile dysfunction (ED). We aimed to evaluate the correlation between 4 urinary organophosphate insecticide metabolites and the presence of ED in a representative sample of men aged 20 and older.

Comprehensive analysis of complete chloroplast genome and phylogenetic aspects of ten Ficus species.

Background: The large genus Ficus comprises approximately 800 species, most of which possess high ornamental and ecological values. However, its evolutionary history remains largely unknown. Plastome (chloroplast genome) analysis had become an essential tool for species identification and for unveiling evolutionary relationships between species, genus and other rank groups.

Metabolic stimulation-elicited transcriptional responses and biosynthesis of acylated triterpenoids precursors in the medicinal plant Helicteres angustifolia.

Background: Helicteres angustifolia has long been used in Chinese traditional medicine. It has multiple pharmacological benefits, including anti-inflammatory, anti-viral and anti-tumor effects. Its main active chemicals include betulinic acid, oleanolic acid, helicteric acid, helicterilic acid, and other triterpenoid saponins.

Effects of Different Molecular Weight Polysaccharides From Kimura & Migo on Human Colorectal Cancer and Transcriptome Analysis of Differentially Expressed Genes.

We investigated the antitumor effects of four fractions of Kimura & Migo (. ) polysaccharides with different molecular weights (Mw), polysaccharides (APS) and polysaccharides (LNT) on colorectal cancer (CRC) using a zebrafish xenograft model. Transcriptome sequencing was performed to further explore the possible antitumor mechanisms of .

Comparative genomic study on the complete plastomes of four officinal Ardisia species in China.

Ardisia Sw. (Primulaceae) is naturally distributed in tropical and subtropical areas. Most of them possess edible and medicinal values and are popular in clinical and daily use in China.

Genome-Wide Identification and Functional Characterization of the Trans-Isopentenyl Diphosphate Synthases Gene Family in .

Trans-isopentenyl diphosphate synthases (TIDSs) genes are known to be important determinants for terpene diversity and the accumulation of terpenoids. The essential oil of , which is rich in monoterpenes, sesquiterpenes, and other aromatic compounds, has a wide range of pharmacological activities and has therefore attracted considerable interest. However, the gene family, and its relationship to the camphor tree ( L.

Metabolism and transcriptome profiling provides insight into the genes and transcription factors involved in monoterpene biosynthesis of borneol chemotype of induced by mechanical damage.

Background: The borneol chemotype of (), a monoterpene-rich woody plant species, is the sole source prescribed by the Chinese Pharmacopoeia for the production of natural D-borneol, a major monoterpene in used for millennia as a topical analgesic in China. Nevertheless, the possible gene-regulatory roles of transcription factors (TFs) in 's monoterpenoid biosynthesis remained unknown. Here, a joint analysis of the transcriptome and terpenoid metabolome of induced by mechanical damage (MD) was used to comprehensively explore the interaction between TFs and terpene synthase (TPS) unigenes that might participate in monoterpene biosynthesis in .

Characterization of the Complete Chloroplast Genome of Buddleja lindleyana.

Background: Buddleja lindleyana Fort., which belongs to the Loganiaceae with a distribution throughout the tropics, is widely used as an ornamental plant in China. There are several morphologically similar species in the genus Buddleja, but the lack of comprehensive molecular and phylogenetic studies makes it difficult to distinguish related species, which hinders further studies of this genus.

Mining of candidate genes involved in the biosynthesis of dextrorotatory borneol in by transcriptomic analysis on three chemotypes.

Background: Dextrorotatory borneol (D-borneol), a cyclic monoterpene, is widely used in traditional Chinese medicine as an efficient topical analgesic drug. Fresh leaves of trees, e.g.

Characteristics analysis of the complete chloroplast genome.

, which belongs to the huge family Zingiberaceae, is used in the clinic for the treatment of spleen and stomach diseases in southern China. The complete chloroplast genome of was sequenced and analyzed using next-generation sequencing technology in the present work. The results showed that the chloroplast genome is a circular molecule with 163,608 bp in length.