ER regulates an evolutionarily conserved apoptosis pathway

Explainable coronary artery disease prediction model based on AutoGluon from AutoML framework

Objective

This study focuses on the innovative application of Automated Machine Learning (AutoML) technology in cardiovascular medicine to construct an explainable Coronary Artery Disease (CAD) prediction model to support the clinical diagnosis of CAD.

Methods

This study utilizes a combined data set of five public data sets related to CAD. An ensemble model is constructed using the AutoML open-source framework AutoGluon to evaluate the feasibility of AutoML in constructing a disease prediction model in cardiovascular medicine. The performance of the ensemble model is compared against individual baseline models. Finally, the disease prediction ensemble model is explained using SHapley Additive exPlanations (SHAP).

Results

The experimental results show that the AutoGluon-based ensemble model performs better than the individual baseline models in predicting CAD. It achieved an accuracy of 0.9167 and an AUC of 0.9562 in 4-fold cross-bagging. SHAP measures the importance of each feature to the prediction of the model and explains the prediction results of the model.

Conclusion

This study demonstrates the feasibility and efficacy of AutoML technology in cardiovascular medicine and highlights its potential in disease prediction. AutoML reduces the barriers to model building and significantly improves prediction accuracy. Additionally, the integration of SHAP enhances model transparency and explainability, which is critical to ensuring model credibility and widespread adoption in cardiovascular medicine.

piRNAs as emerging biomarkers and physiological regulatory molecules in cardiovascular disease

Cardiovascular diseases (CVD) represent one of the most considerable global health threats, owing to their high incidence and mortality rates. Despite the ongoing advancements in detection, prevention, treatment, and prognosis of CVD, which have resulted in a decline in both incidence and mortality rates, CVD remains a major public health concern. Therefore, novel diagnostic biomarkers and therapeutic interventions are imperative to minimise the risk of CVD. Non-coding RNAs (ncRNAs) have recently gained increasing attention, with PIWI-interacting RNAs (piRNAs) emerging as a class of small ncRNAs traditionally recognised for their role in silencing transposons within cells. Although the functional roles of PIWI proteins and piRNAs in human cells remain unclear, growing evidence suggests that these molecules are gradually becoming valuable biomarkers for the diagnosis and treatment of CVD. This review provides a comprehensive summary of the latest studies on piRNAs in CVD. This review discusses the roles of piRNAs in various cardiovascular subtypes, including myocardial hypertrophy, heart failure, myocardial infarction, and cardiac regeneration. The perceived insights may contribute novel perspectives for the diagnosis and treatment of CVD.

Applications of Network Pharmacology in Traditional Chinese Medicine Research

Human diseases, especially infectious ones, have been evolving constantly. However, their treatment strategies are not developing quickly. Some diseases are caused by a variety of factors with very complex pathologies, and the use of a single drug cannot solve these problems. Traditional Chinese Medicine (TCM) medication is a unique treatment method in China. TCM formulae contain multiple herbs with multitarget, multichannel, and multilink characteristics. In recent years, with the flourishing development of network pharmacology, a new method for searching therapeutic drugs has emerged. The multitarget action in network pharmacology is consistent with the complex mechanisms of disease and drug action. Using network pharmacology to understand TCM is an emerging trend.

FOXA1 is Prognostic of Triple Negative Breast Cancers by Transcriptionally Suppressing SOD2 and IL6

Having markers feasible for breast cancer subtyping, especially for triple negative breast cancer identification is crucial for improving the treatment outcome of such cancers. Here we explore the role of FOXA1 in characterizing triple negative breast cancers and the driving mechanisms. Through in vitro examination of the expression pattern at both transcriptional and translational levels, patient relapse-free survival analysis, immunohistochemistry staining and prediction power assessment using clinical samples, as well as functional studies, we systematically compared the role of FOXA1 in identifying triple negative and luminal type of breast cancers and explored the mechanisms driving such functionalities. We report that FOXA1 under-expression can lead to increased malignancy and cancer stemness, and is a subtyping marker identifying triple negative breast cancers rather than the luminal subtype by transcriptionally suppressing the expression of SOD2 and IL6. We are the first to systematically address the significance of FOXA1 in triple negative breast cancer identification as a biomarker and elucidate the mechanism at the molecular level, through a sequential bioinformatics analysis and experimental validations both in vitro and in clinics. Our discoveries compliment the current biomarker modalities once verified using larger clinical cohorts and improve the precision on characterizing breast cancer heterogeneity.

Investigating Common Pathogenic Mechanisms between Homo sapiens and Different Strains of Candida albicans for Drug Design: Systems Biology Approach via Two-Sided NGS Data Identification

Candida albicans (C. albicans) is the most prevalent fungal species. Although it is a healthy microbiota, genetic and epigenetic alterations in host and pathogen, and microenvironment changes would lead to thrush, vaginal yeast infection, and even hematogenously disseminated infection. Despite the fact that cytotoxicity is well-characterized, few studies discuss the genome-wide genetic and epigenetic molecular mechanisms between host and C. albicans. The aim of this study is to identify drug targets and design a multiple-molecule drug to prevent the infection from C. albicans. To investigate the common and specific pathogenic mechanisms in human oral epithelial OKF6/TERT-2 cells during the C. albicans infection in different strains, systems modeling and big databases mining were used to construct candidate host–pathogen genetic and epigenetic interspecies network (GEIN). System identification and system order detection are applied on two-sided next generation sequencing (NGS) data to build real host–pathogen cross-talk GEINs. Core host–pathogen cross-talk networks (HPCNs) are extracted by principal network projection (PNP) method. By comparing with core HPCNs in different strains of C. albicans, common pathogenic mechanisms were investigated and several drug targets were suggested as follows: orf19.5034 (YBP1) with the ability of anti-ROS; orf19.939 (NAM7), orf19.2087 (SAS2), orf19.1093 (FLO8) and orf19.1854 (HHF22) with high correlation to the hyphae growth and pathogen protein interaction; orf19.5585 (SAP5), orf19.5542 (SAP6) and orf19.4519 (SUV3) with the cause of biofilm formation. Eventually, five corresponding compounds—Tunicamycin, Terbinafine, Cerulenin, Tetracycline and Tetrandrine—with three known drugs could be considered as a potential multiple-molecule drug for therapeutic treatment of C. albicans.

Effects of common polymorphism rs11614913 in Hsa-miR-196a2 on lung cancer risk

Background

Emerging evidence suggests that single nucleotide polymorphisms (SNPs) in microRNA-coding genes may participate in the pathogenesis of lung cancer by altering the expression of tumor-related microRNAs. Several studies were investigated in recent years to evaluate the association between hsa-miR-196a2 rs11614913 polymorphism and increased/decreased lung cancer risk. In the present study, we performed a meta-analysis to systematically summarize the possible association.

Methodology/Principal Findings

We performed a meta-analysis of 4 case-control studies that included 2219 lung-cancer cases and 2232 cancer-free controls. We evaluated the strength of the association using odds ratios (ORs) with 95% confidence intervals (CIs). In the overall analysis, it was found that the rs11614913 polymorphism significantly elevated the risk of lung cancer (CC versus (vs.) TT OR = 1.26, 95% CI 1.07–1.49, P = 0.007; CC/CT vs. TT: OR = 1.13, 95% CI 0.98–1.29, P = 0.007; C vs. T: OR = 1.12, 95% CI 1.03–1.22, P = 0.008). In the subgroup analysis by ethnicity, statistically significantly increased cancer risk was found among Asians (CC vs. TT: OR = 1.30, 95% CI 1.10–1.54, P = 0.003; CT vs. TT: OR = 1.16, 95% CI 1.01–1.34, P = 0.039; CC vs. CT/TT: OR = 1.21, 95% CI 1.04–1.41, P = 0.012; C vs. T: OR = 1.14, 95% CI 1.05–1.25, P = 0.002). For Europeans, a significant association with lung cancer risk was found in recessive model (CC vs. CT/TT: OR = 0.63, 95% CI 0.40–0.98, P = 0.040). No publication bias was found in this study.

Conclusions/Significance

Our meta-analysis suggests that the rs11614913 polymorphism is significant associated with the increased risk of lung cancer, especially in Asians. Besides, the C allele of rs11614913 polymorphism may contribute to increased lung cancer risk.

Assessment of phylogenetic relationship of rare plant species collected from Saudi Arabia using internal transcribed spacer sequences of nuclear ribosomal DNA

The rare and endangered plants of any country are important genetic resources that often require urgent conservation measures. Assessment of phylogenetic relationships and evaluation of genetic diversity is very important prior to implementation of conservation strategies for saving rare and endangered plant species. We used internal transcribed spacer sequences of nuclear ribosomal DNA for the evaluation of sequence identity from the available taxa in the GenBank database by using the Basic Local Alignment Search Tool (BLAST). Two rare plant species viz, Heliotropium strigosum claded with H. pilosum (98% branch support) and Pancratium tortuosum claded with P. tenuifolium (61% branch support) clearly. However, some species, viz Scadoxus multiflorus, Commiphora myrrha and Senecio hadiensis showed close relationships with more than one species. We conclude that nuclear ribosomal internal transcribed spacer sequences are useful markers for phylogenetic study of these rare plant species in Saudi Arabia.

Bioinformatic analysis of chemokine (C-C motif) ligand 21 and SPARC-like protein 1 revealing their associations with drug resistance in ovarian cancer

Chemokine (C-C motif) ligand 21 (CCL21) and SPARC-like protein 1 (SPARCL1/MAST9/hevin/SC-1) are associated with various biological behavior in the development of cancers. Although the expression of CCL21 and SPARCL1 is downregulated in many solid tumors, their roles in ovarian cancer and their associations with drug resistance have rarely been studied. We performed a comprehensive bioinformatic analysis consisting of motif analysis, literature co-occurrence, gene/protein-gene/protein interaction network, protein-small molecule interaction network, and microRNAs enrichments which revealed that CCL21 and SPARCL1 directly or indirectly interact with a number of genes, proteins, small molecules and pathways associated with drug resistance in ovarian and other cancers. These results suggested that CCL21 and SPARCL1 may contribute to drug resistance in ovarian cancer. This study provided important information for further investigation of drug resistance-related functions of CCL21 and SPARCL1 in ovarian cancer.

HRAS: a webserver for early warning of human health risk brought by aflatoxin

Most people are aware that outdoor air pollution can damage their health, but many do not know that indoor air pollution can also exhibit significant negative health effects. Fungi parasitizing in air conditioning and ventilation systems can be one of indoor air pollution sources. Aflatoxin produced by Aspergillus flavus (A. flavus) became a central focus of indoor air pollution, especially in farmer markets. Therefore we developed an early warning system, Health Risk Assessment System, to estimate the growth rate of A. flavus, predict the amount of aflatoxin and provide early warning information. Firstly, the growth of A. flavus and the production of aflatoxin under different conditions were widely obtained through a comprehensive literature review. Secondly, three mathematical models were established to predict the A. flavus colony growth rate, lag phase duration and aflatoxin content, as functions of temperature and water activity based on present studies. Finally, all the results were evaluated by the user-supplied data using PHP programming language. We utilized the web page to show the results and display warning information. The JpGraph library was used to create a dynamic line chart, refreshing the warning information dynamically in real-time. The HARS provides accurate information for early warning purposes to let us take timely steps to protect ourselves.

Ischemia/reperfusion-induced MKP-3 impairs endothelial NO formation via inactivation of ERK1/2 pathway

Mitogen-activated protein kinase phosphatases (MKPs) are a family of dual-specificity phosphatases. Endothelial cells express multiple MKP family members, such as MKP-3. However, the effects of MKP-3 on endothelial biological processes have not yet been fully elucidated. Here, we address the association between MKP-3 and endothelial Nitric oxide (NO) formation under ischemia/reperfusion (IS/RP) condition. Human umbilical vein endothelial cells (HUVECs) were subjected to IS/RP treatment. The MKP-3 expression and NO formation were examined. IS/RP induced endothelial MKP-3 expression and inhibited eNOS expression and NO formation, accompanied by an increase of endothelial apoptosis. The siRNA experiments showed that MKP-3 was an important mediator in impairing eNOS expression and NO production in endothelial cells. Transfection of HUVECs with constitutively active ERK plasmids suggested that the above mentioned effect of MKP-3 was via inactivation of ERK1/2 pathway. Furthermore, impairment of eNOS expression was restored by treatment of histone deacetylase (HDAC) inhibitor and related to histone deacetylation and recruitment of HDAC1 to the eNOS promoter. Finally, Salvianolic acid A (SalA) markedly attenuated induction of MKP-3 and inhibition of eNOS expression and NO formation under endothelial IS/RP condition. Overall, these results for the first time demonstrated that IS/RP inhibited eNOS expression by inactivation of ERK1/2 and recruitment of HDAC1 to the gene promoter, leading to decreased NO formation through a MKP-3-dependent mechanism in endothelial cells, and SalA has therapeutic significance in protecting endothelial cells from impaired NO formation in response to IS/RP.

Identification of medicinal vines by ITS2 using complementary discrimination methods

ETHNOPHARMACOLOGICAL RELEVANCE

Medicinal vines listed in Chinese pharmacopoeia possess important medicinal efficacy in traditional Chinese medicines.

AIM OF THE STUDY

The ITS2 region, which has several characteristics that make it a valuable DNA barcode, was studied to discriminate the stems of medicinal vines to confirm their identities and ensure their safe application in pharmaceuticals by using complementary discrimination methods.

MATERIALS AND METHODS

Complementary discrimination methods were performed on two datasets, including 393 samples of 170 species from 22 genera 13 families, which belonged to medicinal vines and their adulterants. Based on the primary ITS2 sequences, three main discrimination methods (phylogenetic tree, the nearest distance, and BLAST 1) were adopted to identify species. Moreover, we applied both two-dimensional (2-D) and three-dimensional (3-D) structures of ITS2 to differentiate species.

RESULTS

ITS2 performed well, with over 95.0% of species and 100% of genera being correctly differentiated for the two datasets. All results showed that the ITS2 region unveiled a remarkable ability to identify closely related species within different families and genera.

CONCLUSION

Our findings supported that the ITS2 region was an efficient marker for authentication of medicinal vines.

BRCA1: a new candidate gene for bovine mastitis and its association analysis between single nucleotide polymorphisms and milk somatic cell score

Bovine mastitis is a very complex and common disease of dairy cattle and a major source of economic losses to the dairy industry worldwide. In this study, the bovine breast cancer 1, early onset gene (BRCA1) was taken as a candidate gene for mastitis resistance. The main object of this study was to investigate whether the BRCA1 gene was associated with mastitis in cattle. Through DNA sequencing, Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) and Created Restriction Site PCR (CRS-PCR) methods, three SNPs (G22231T, T25025A, and C28300A) were detected and twenty-four combinations of these SNPs were observed. The single SNP and their genetic effects on somatic cell score (SCS) were evaluated and a significant association with SCS was found in C28300A. The mean of genotype EE was significantly lower than those of genotypes EF and FF. The results of combined genotypes analysis of three SNPs showed that BBDDFF genotype with the highest SCS were easily for the mastitis susceptibility, whereas AACCEE genotype with the lowest SCS were favorable for the mastitis resistance. The information provided in the present study will be very useful for improving mastitis resistance in dairy cattle by marker-assisted selection.

Phylogenetic study of Oryzoideae species and related taxa of the Poaceae based on atpB-rbcL and ndhF DNA sequences

Oryzoideae (Poaceae) plants have economic and ecological value. However, the phylogenetic position of some plants is not clear, such as Hygroryza aristata (Retz.) Nees. and Porteresia coarctata (Roxb.) Tateoka (syn. Oryza coarctata). Comprehensive molecular phylogenetic studies have been carried out on many genera in the Poaceae. The different DNA sequences, including nuclear and chloroplast sequences, had been extensively employed to determine relationships at both higher and lower taxonomic levels in the Poaceae. Chloroplast DNA ndhF gene and atpB-rbcL spacer were used to construct phylogenetic trees and estimate the divergence time of Oryzoideae, Bambusoideae, Panicoideae, Pooideae and so on. Complete sequences of atpB-rbcL and ndhF were generated for 17 species representing six species of the Oryzoideae and related subfamilies. Nicotiana tabacum L. was the outgroup species. The two DNA datasets were analyzed, using Maximum Parsimony and Bayesian analysis methods. The molecular phylogeny revealed that H. aristata (Retz.) Nees was the sister to Chikusichloa aquatica Koidz. Moreover, P. coarctata (Roxb.) Tateoka was in the genus Oryza. Furthermore, the result of evolution analysis, which based on the ndhF marker, indicated that the time of origin of Oryzoideae might be 31 million years ago.