Identification and Validation of an 11-Ferroptosis Related Gene Signature and Its Correlation With Immune Checkpoint Molecules in Glioma

BackgroundGlioma is the most common primary malignant brain tumor with significant mortality and morbidity. Ferroptosis, a novel form of programmed cell death (PCD), is critically involved in tumorigenesis, progression and metastatic processes.MethodsWe revealed the relationship between ferroptosis-related genes and glioma by analyzing the mRNA expression profiles from The Cancer Genome Atlas (TCGA), Chinese Glioma Genome Atlas (CGGA), GSE16011, and the Repository of Molecular Brain Neoplasia Data (REMBRANDT) datasets. The least absolute shrinkage and selection operator (LASSO) Cox regression analysis was performed to construct a ferroptosis-associated gene signature in the TCGA cohort. Glioma patients from the CGGA, GSE16011, and REMBRANDT cohorts were used to validate the efficacy of the signature. Receiver operating characteristic (ROC) curve analysis was applied to measure the predictive performance of the risk score for overall survival (OS). Univariate and multivariate Cox regression analyses of the 11-gene signature were performed to determine whether the ability of the prognostic signature in predicting OS was independent. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted to identify the potential biological functions and pathways of the signature. Subsequently, we performed single sample gene set enrichment analysis (ssGSEA) to explore the correlation between risk scores and immune status. Finally, seven putative small molecule drugs were predicted by Connectivity Map.ResultsThe 11-gene signature was identified to divide patients into two risk groups. ROC curve analysis indicated the 11-gene signature as a potential diagnostic factor in glioma patients. Multivariate Cox regression analyses showed that the risk score was an independent predictive factor for overall survival. Functional analysis revealed that genes were enriched in iron-related molecular functions and immune-related biological processes. The results of ssGSEA indicated that the 11-gene signature was correlated with the initiation and progression of glioma. The small molecule drugs we selected showed significant potential to be used as putative drugs.Conclusionwe identified a novel ferroptosis-related gene signature for prognostic prediction in glioma patients and revealed the relationship between ferroptosis-related genes and immune checkpoint molecules

Adaptive Tuning of Robotic Polishing Skills based on Force Feedback Model

Acquiring human skills offers an efficient approach to tackle complex task planning challenges. When performing a learned skill model for a continuous contact task, such as robot polishing in an uncertain environment, the robot needs to be able to adaptively modify the skill model to suit the environment and perform the desired task. The environmental perturbation of the polishing task is mainly reflected in the variation of contact force. Therefore, adjusting the task skill model by providing feedback on the contact force deviation is an effective way to meet the task requirements. In this study, a phase-modulated diagonal recurrent neural network (PMDRNN) is proposed for force feedback model learning in the robotic polishing task. The contact between the tool and the workpiece in the polishing task can be considered a dynamic system. In comparison to the existing feedforward neural network phase-modulated neural network (PMNN), PMDRNN combines the diagonal recurrent network structure with the phase-modulated neural network layer to improve the learning performance of the feedback model for dynamic systems. Specifically, data from real-world robot polishing experiments are used to learn the feedback model. PMDRNN demonstrates a significant reduction in the training error of the feedback model when compared to PMNN. Building upon this, the combination of PMDRNN and dynamic movement primitives (DMPs) can be used for real-time adjustment of skills for polishing tasks and effectively improve the robustness of the task skill model. Finally, real-world robotic polishing experiments are conducted to demonstrate the effectiveness of the approach.Comment: This paper has been accepted by The 2023 IEEE International Conference on Robotics and Biomimetics (IEEE ROBIO 2023

Eclipsing Binaries From the CSTAR Project at Dome A, Antarctica

The Chinese Small Telescope ARray (CSTAR) has observed an area around the Celestial South Pole at Dome A since 2008. About $20,000$ light curves in the i band were obtained lasting from March to July, 2008. The photometric precision achieves about 4 mmag at i = 7.5 and 20 mmag at i = 12 within a 30 s exposure time. These light curves are analyzed using Lomb--Scargle, Phase Dispersion Minimization, and Box Least Squares methods to search for periodic signals. False positives may appear as a variable signature caused by contaminating stars and the observation mode of CSTAR. Therefore the period and position of each variable candidate are checked to eliminate false positives. Eclipsing binaries are removed by visual inspection, frequency spectrum analysis and locally linear embedding technique. We identify 53 eclipsing binaries in the field of view of CSTAR, containing 24 detached binaries, 8 semi-detached binaries, 18 contact binaries, and 3 ellipsoidal variables. To derive the parameters of these binaries, we use the Eclipsing Binaries via Artificial Intelligence (EBAI) method. The primary and the secondary eclipse timing variations (ETVs) for semi-detached and contact systems are analyzed. Correlated primary and secondary ETVs confirmed by false alarm tests may indicate an unseen perturbing companion. Through ETV analysis, we identify two triple systems (CSTAR J084612.64-883342.9 and CSTAR J220502.55-895206.7). The orbital parameters of the third body in CSTAR J220502.55-895206.7 are derived using a simple dynamical model.Comment: 41 pages, 12 figures; published online in ApJ

Comprehensive analyses indicated the association between m6A related long non‐coding RNAs and various pathways in glioma

Abstract Background Glioma is one of the most malignant brain tumors and diseases. N6‐methyladenosine modification (m6A) is the most abundant and prevalent internal chemical modification of mRNA and long non‐coding RNAs (lncRNAs) in eukaryotes. Nevertheless, the correlated pathways and clinical utilization of m6A‐related lncRNAs have not been fully evaluated in glioma. Methods Public RNA‐sequencing and clinical annotation data were retrieved from TCGA, CGGA and GEO database. Differential expression analysis and univariate Cox regression analysis were performed to identify the m6A‐related and differentially expressed lncRNAs with prognostic function (m6A‐DELPF). The consensus clustering was performed to identify the expression pattern of m6A‐DELPF. LASSO Cox regression analysis was performed to construct the lncRNA‐based signature. The CIBERSORT and ESTIMATE algorithms were performed to analyze immune infiltration and tumor microenvironment, respectively. Immunotherapy sensitivity analysis was performed using data from TCIA. The small molecule drugs prediction analysis was performed using The Connectivity Map (CMap) database and STITCH database. A competing endogenous RNAs (ceRNA) network was constructed based on miRcode, miRDB, miRTarBase, TargetScan database. Results Two clusters (cluster1 and cluster2) were identified after unsupervised cluster analysis based on m6A‐DELPF. Additionally, a 15‐gene prognostic signature namely m6A‐DELPFS was constructed. Analyses of epithelial‐mesenchymal‐transition score, tumor microenvironment, immune infiltration, clinical characterization analysis, and putative drug prediction were performed to confirm the clinical utility and efficacy of m6A‐DELPFS. The potential mechanisms including tumor immune microenvironment of m6A‐DELPF influence the initiation and progression of glioma. A clinically accessible nomogram was also constructed based on the m6A‐DELPF and other survival‐relevant clinical parameters. Two miRNAs and 114 mRNAs were identified as the downstream of seven m6A‐related lncRNAs in a ceRNA network. Conclusion Our present research confirmed the clinical value of m6A related lncRNAs and their high correlation with tumor immunity, tumor microenvironment, tumor mutation burden and drug sensitivity in glioma

Peptide ligand-SiO2 microspheres with specific affinity for phosphatidylserine as a new strategy to isolate exosomes and application in proteomics to differentiate hepatic cancer

Exosomes are membrane bound extracellular vesicles that play an important role in many biological processes. While they have great application value, exosome isolation is still considered a major scientific challenge. In the present study, a novel separation strategy for exosomes is proposed based on the specific interaction between immobilized peptide ligands and phosphatidylserine moieties which are highly abundant on the surface of exosomes. With the new affinity method, intact model exosomes can be recovered with a high yield in a short processing time. The purity of exosome samples enriched from serum by the affinity method is far higher than that isolated by ultrafiltration, and similar to that obtained by density gradient centrifugation and ultracentrifugation. Moreover, the variety of contaminants co-isolated by the affinity method is relatively low due to its specific separation principle. Proteomics analysis of exosomes isolated by the affinity method from the serum of healthy, hepatocellular carcinoma patients, and intrahepatic cholangiocarcinoma patients was performed to prove the applicability of this method. In conclusion, our novel strategy shows characteristics of easy preparation, high specificity, and cost-effectiveness, and provides a promising approach for exosome isolation which should have wide applications

Melanin-Associated Synthesis of SERS-Active Nanostructures and the Application for Monitoring of Intracellular Melanogenesis

Melanin plays an indispensable role in the human body. It serves as a biological reducer for the green synthesis of precious metal nanoparticles. Melanin–Ag nanocomposites were successfully produced which exhibited very strong surface-enhanced Raman scattering (SERS) effect because of the reducibility property of melanin. A melanin–Ag composite structure was synthesized in situ in melanin cells, and SERS technique was performed for the rapid imaging and quantitative assay of intracellular melanin. This imaging technique was also used to successfully trace the formation and secretion of intracellular melanin after stimulation with melanin-stimulating hormones. Based on the self-reducing property of melanin, the proposed SERS imaging method can provide potentially powerful analytical detection tools to study the biological functions of melanin and to prevent and cure melanin-related diseases

In Vivo Detection of the Effect of Electroacupuncture on “Zusanli” Acupoint in Rats with Adjuvant-Induced Arthritis through Optical Coherence Tomography

This study aimed to investigate the effect of electroacupuncture (EA) treatment through optical coherence tomography (OCT) in vivo on rats with adjuvant-induced arthritis. OCT images were obtained from the ankle of the right hind paws of the rats in control, model, and EA groups before modelling and 1 day, 8 days, 15 days, 22 days, and 29 days after modelling. Results demonstrated that the OCT signal of the ankle of the right hind paws of the rats was indistinct compared to 1 day after modelling and before modelling in the EA group. In the EA group, the light averaged attenuation coefficients of the ankle tissues decreased as treatment duration was prolonged after EA was administered (3.43, 2.96, 2.61, 2.42, and 2.29 mm−1, resp.). There was a significant difference in attenuation coefficient decrease between the 29th d and the 1st d for EA group compared with control group (P<0.01). This condition indicated that the light absorption of the ankle of the treated rats in the EA group decreased. Therefore, OCT can be used to monitor the effect of treatment on rats with arthritis in vivo

Table_1_Bioinformatics and systems-biology analysis to determine the effects of Coronavirus disease 2019 on patients with allergic asthma.docx

BackgroundThe coronavirus disease (COVID-19) pandemic has posed a significant challenge for global health systems. Increasing evidence shows that asthma phenotypes and comorbidities are major risk factors for COVID-19 symptom severity. However, the molecular mechanisms underlying the association between COVID-19 and asthma are poorly understood. Therefore, we conducted bioinformatics and systems biology analysis to identify common pathways and molecular biomarkers in patients with COVID-19 and asthma, as well as potential molecular mechanisms and candidate drugs for treating patients with both COVID-19 and asthma.MethodsTwo sets of differentially expressed genes (DEGs) from the GSE171110 and GSE143192 datasets were intersected to identify common hub genes, shared pathways, and candidate drugs. In addition, murine models were utilized to explore the expression levels and associations of the hub genes in asthma and lung inflammation/injury.ResultsWe discovered 157 common DEGs between the asthma and COVID-19 datasets. A protein–protein-interaction network was built using various combinatorial statistical approaches and bioinformatics tools, which revealed several hub genes and critical modules. Six of the hub genes were markedly elevated in murine asthmatic lungs and were positively associated with IL-5, IL-13 and MUC5AC, which are the key mediators of allergic asthma. Gene Ontology and pathway analysis revealed common associations between asthma and COVID-19 progression. Finally, we identified transcription factor–gene interactions, DEG–microRNA coregulatory networks, and potential drug and chemical-compound interactions using the hub genes.ConclusionWe identified the top 15 hub genes that can be used as novel biomarkers of COVID-19 and asthma and discovered several promising candidate drugs that might be helpful for treating patients with COVID-19 and asthma.</p