Identification of differentially expressed key genes between glioblastoma and low-grade glioma by bioinformatics analysis

Gliomas are a very diverse group of brain tumors that are most commonly primary tumor and difficult to cure in central nervous system. It’s necessary to distinguish low-grade tumors from high-grade tumors by understanding the molecular basis of different grades of glioma, which is an important step in defining new biomarkers and therapeutic strategies. We have chosen the gene expression profile GSE52009 from gene expression omnibus (GEO) database to detect important differential genes. GSE52009 contains 120 samples, including 60 WHO II samples and 24 WHO IV samples that were selected in our analysis. We used the GEO2R tool to pick out differently expressed genes (DEGs) between low-grade glioma and high-grade glioma, and then we used the database for annotation, visualization and integrated discovery to perform gene ontology analysis and Kyoto encyclopedia of gene and genome pathway analysis. Furthermore, we used the Cytoscape search tool for the retrieval of interacting genes with molecular complex detection plug-in applied to achieve the visualization of protein–protein interaction (PPI). We selected 15 hub genes with higher degrees of connectivity, including tissue inhibitors metalloproteinases-1 and serum amyloid A1; additionally, we used GSE53733 containing 70 glioblastoma samples to conduct Gene Set Enrichment Analysis. In conclusion, our bioinformatics analysis showed that DEGs and hub genes may be defined as new biomarkers for diagnosis and for guiding the therapeutic strategies of glioblastoma

NH2+ implantations induced superior hemocompatibility of carbon nanotubes

NH(2)(+) implantation was performed on multiwalled carbon nanotubes (MWCNTs) prepared by chemical vapor deposition. The hemocompatibility of MWCNTs and NH(2)(+)-implanted MWCNTs was evaluated based on in vitro hemolysis, platelet adhesion, and kinetic-clotting tests. Compared with MWCNTs, NH(2)(+)-implanted MWCNTs displayed more perfect platelets and red blood cells in morphology, lower platelet adhesion rate, lower hemolytic rate, and longer kinetic blood-clotting time. NH(2)(+)-implanted MWCNTs with higher fluency of 1 × 10(16) ions/cm(2) led to the best thromboresistance, hence desired hemocompatibility. Fourier transfer infrared and X-ray photoelectron spectroscopy analyses showed that NH(2)(+) implantation caused the cleavage of some pendants and the formation of some new N-containing functional groups. These results were responsible for the enhanced hemocompatibility of NH(2)(+)-implanted MWCNTs

Identification of pivotal genes and regulatory networks associated with atherosclerotic carotid artery stenosis based on comprehensive bioinformatics analysis and machine learning

Objective:Bioinformatics methods were applied to investigate the pivotal genes and regulatory networks associated with atherosclerotic carotid artery stenosis (ACAS) and provide new insights for the treatment of this disease.Methods:The study utilized five ACAS datasets (GSE100927, GSE11782, GESE28829, GSE41571, and GSE43292) downloaded from the NCBI GEO database. The first four datasets were combined as the training set (n = 99), while GSE43292 (n = 64) was used as the validation set. Difference analysis and functional enrichment analysis were then performed on the training set. The pathogenic targets of ACAS were screened by protein-protein interaction networks and MCODE analyses, combined with three machine learning algorithms. The results were next verified by analysis of inter-group differences and ROC curve analysis. Next, immune-related function and immune cell correlation analyses were performed, and plaques of human ACAS were applied to verify the results via immunohistochemistry (IH) and immunofluorescence (IF). Finally, the competing endogenous RNAs (ceRNA) and transcription factors (TFs) regulatory networks of the characterized genes were constructed.Results:A total of 177 differentially expressed genes were identified, including 67 genes downregulated and 110 genes upregulated. Gene set enrichment analysis revealed that five pathways were active in the experimental group, including xenograft rejection, autoimmune thyroid disease, graft-versus-host disease, leishmaniasis infection, and lysosomes. Four key genes were identified, with C3AR1 being upregulated and FBLN5, PPP1R12A, and TPM1 being downregulated. The analysis of inter-group differences demonstrated that the four characterized genes were differentially expressed in both the control and experimental groups. The ROC analysis showed that they had high AUC values in both the training and validation sets. Therefore, a predictive ACAS patient nomogram model based on the screened genes was established. Correlation analysis revealed a positive correlation between C3AR1 expression and neutrophils, which was further validated in IH and IF. One or multiple lncRNAs may compete with the characterized genes for binding miRNAs. Additionally, each characterized gene interacts with multiple TFs.Conclusion:Four pivotal genes were screened, and relevant ceRNA and TFs were predicted. These molecules may exert a crucial role in ACAS and serve as potential biomarkers and therapeutic targets

TPH-2 Gene Polymorphism in Major Depressive Disorder Patients With Early-Wakening Symptom

Background: Sleep disturbances, such as early wakening, are frequently observed in patients with major depressive disorder (MDD). The suprachiasmatic nuclei (SCN), which controls circadian rhythm, is innervated by the raphe nucleus, a region where Tryptophan hydroxylase-2 (TPH-2) gene is primarily expressed. Although TPH-2 is often implicated in the pathophysiology of depression, few studies have applied a genetic and imaging technique to investigate the mechanism of early wakening symptom in MDD. We hypothesized that TPH-2 variants could influence the function of SCN in MDD patients with early wakening symptom.Methods: One hundred and eighty five MDD patients (62 patients without early wakening and 123 patients with early wakening) and 64 healthy controls participated in this study. Blood samples were collected and genotyping of rs4290270, rs4570625, rs11178998, rs7305115, rs41317118, and rs17110747 were performed by next-generation sequencing (NGS) technology. Logistic regression model was employed for genetic data analysis using the PLINK software. Based on the allele type, rs4290270, which was significant in the early wakening MDD group, participants were categorized into two groups (A allele and T carrier). All patients underwent whole brain resting-state functional magnetic resonance imaging (rs-fMRI) scanning and a voxel-wise functional connectivity comparison was performed between the groups.Results: rs4290270 was significantly linked to MDD patients who exhibited early wakening symptom. The functional connectivities of the right SCN with the right fusiform gyrus and right middle frontal gyrus were increased in the T carrier group compared to the A allele group. In addition, the functional connectivities of the left SCN with the right lingual gyrus and left calcarine sulcus were decreased in the T carrier group compared to the A allele group.Conclusion: These findings suggested that the TPH-2 gene variant, rs4290270, affected the circadian regulating function of SCN. The altered functional connectivities, observed between the SCN and right fusiform gyrus, right middle frontal gyrus, the right lingual gyrus and left calcarine sulcus, could highlight the neural mechanism by which SCN induces sleep-related circadian disruption in T carrier MDD patients. Hence, rs4290270 could potentially serve as a reliable biomarker to identify MDD patients with early wakening symptom

Differentiation of Transformed Bipolar Disorder From Unipolar Depression by Resting-State Functional Connectivity Within Reward Circuit

Previous studies have found that neural functional abnormalities detected by functional magnetic resonance imaging (fMRI) in brain regions implicated in reward processing during reward tasks show promise to distinguish bipolar from unipolar depression (UD), but little is known regarding resting-state functional connectivity (rsFC) within the reward circuit. In this study, we investigated neurobiomarkers for early recognition of bipolar disorder (BD) by retrospectively comparing rsFC within the reward circuit between UD and depressed BD. Sixty-six depressed patients were enrolled, none of whom had ever experienced any manic/hypomanic episodes before baseline. Simultaneously, 40 matched healthy controls (HC) were also recruited. Neuroimaging data of each participant were obtained from resting-state fMRI scans. Some patients began to manifest bipolar disorder (tBD) during the follow-up period. All patients were retrospectively divided into two groups (33 tBD and 33 UD) according to the presence or absence of mania/hypomania in the follow-up. rsFC between key regions of the reward circuit was calculated and compared among groups. Results showed decreased rsFC between the left ventral tegmental area (VTA) and left ventral striatum (VS) in the tBD group compared with the UD group, which showed good accuracy in predicting diagnosis (tBD vs. UD) according to receiver operating characteristic (ROC) analysis. No significant different rsFC was found within the reward circuit between any patient group and HC. Our preliminary findings indicated that bipolar disorder, in early depressive stages before onset of mania/hypomania attacks, already differs from UD in the reward circuit of VTA-VS functional synchronicity at the resting state

Identification of Core Gene Biomarkers in Patients with Diabetic Cardiomyopathy

Diabetic cardiomyopathy (DCM) is a disorder of the myocardium in diabetic patients, which is one of the critical complications of diabetes giving rise to an increased mortality. However, the underlying mechanisms of DCM remain incompletely understood presently. This study was designed to screen the potential molecules and pathways implicated with DCM. GSE26887 involving 5 control individuals and 7 DCM patients was selected from the GEO database to identify the differentially expressed genes (DEGs). DAVID was applied to perform gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. A protein-protein interaction (PPI) network was also constructed to visualize the interactions among these DEGs. To further validate significant genes and pathways, quantitative real-time PCR (qPCR) and Western blot were performed. A total of 236 DEGs were captured, including 134 upregulated and 102 downregulated genes. GO, KEGG, and the PPI network disclosed that inflammation, immune disorders, metabolic disturbance, and mitochondrial dysfunction were significantly enriched in the development of DCM. Notably, IL6 was an upregulated hub gene with the highest connectivity degree, suggesting that it may interact with a great many molecules and pathways. Meanwhile, SOCS3 was also one of the top 15 hub genes in the PPI network. Herein, we detected the protein level of STAT3 and SOCS3 in a mouse model with DCM. Western blot results showed that the protein level of SOCS3 was significantly lower while phosphorylated-STAT3 (P-STAT3) was activated in mice with DCM. In vitro results also uncovered the similar alterations of SOCS3 and P-STAT3 in cardiomyocytes and cardiac fibroblasts induced by high glucose (HG). However, overexpression of SOCS3 could significantly reverse HG-induced cardiomyocyte hypertrophy and collagen synthesis of cardiac fibroblasts. Taken together, our analysis unveiled potential biomarkers and molecular mechanisms in DCM, which could be helpful to the diagnosis and treatment of DCM

Effect of the Abnormal Expression of BMP-4 in the Blood of Diabetic Patients on the Osteogenic Differentiation Potential of Alveolar BMSCs and the Rescue Effect of Metformin: A Bioinformatics-Based Study

The success rate of oral implants is lower in type 2 diabetes mellitus (T2DM) patients than in nondiabetic subjects; functional impairment of bone marrow-derived mesenchymal stem cells (BMSCs) is an important underlying cause. Many factors in the blood can act on BMSCs to regulate their biological functions and influence implant osseointegration, but which factors play important negative roles in T2DM patients is still unclear. This study is aimed at screening differentially expressed genes in the blood from T2DM and nondiabetic patients, identifying which genes impact the osteogenic differentiation potential of alveolar BMSCs in T2DM patients, exploring drug intervention regimens, and providing a basis for improving implant osseointegration. Thus, a whole-blood gene expression microarray dataset (GSE26168) of T2DM patients and nondiabetic controls was analyzed. Based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) results, differentially expressed genes and signaling pathways related to BMSC osteogenic differentiation were screened, and major risk genes were extracted based on the mean decrease Gini coefficient calculated using the random forest method. Bone morphogenetic protein-4 (BMP-4), with significantly low expression in T2DM blood, was identified as the most significant factor affecting BMSC osteogenic differentiation potential. Subsequently, metformin, a first-line clinical drug for T2DM treatment, was found to improve the osteogenic differentiation potential of BMSCs from T2DM patients via the BMP-4/Smad/Runx2 signaling pathway. These results demonstrate that low BMP-4 expression in the blood of T2DM patients significantly hinders the osteogenic function of BMSCs and that metformin is effective in counteracting the negative impact of BMP-4 deficiency

Effectiveness and Mechanisms of Low-Intensity Pulsed Ultrasound on Osseointegration of Dental Implants and Biological Functions of Bone Marrow Mesenchymal Stem Cells

Dental implant restoration is the preferred choice for patients with dentition defects or edentulous patients, and obtaining stable osseointegration is the determining factor for successful implant healing. The risk of implant failure during the healing stage is still an urgent problem in clinical practice due to differences in bone quality at different implant sites and the impact of some systemic diseases on bone tissue metabolism. Low-intensity pulsed ultrasound (LIPUS) is a noninvasive physical intervention method widely recognized in the treatment of bone fracture and joint damage repair. Moreover, many studies indicated that LIPUS could effectively promote the osseointegration of dental implants and improve the osteogenic differentiation of bone marrow mesenchymal stem cells (BMSCs). This review is aimed at investigating the research progress on the use of LIPUS in dental implant medicine from three aspects: (1) discuss the promoting effects of LIPUS on osseointegration and peri-implant bone regeneration, (2) summarize the effects and associated mechanisms of LIPUS on the biological functions of BMSCs, and (3) introduce the application and prospects of LIPUS in the clinical work of dental implantation. Although many challenges need to be overcome in the future, LIPUS is bound to be an efficient and convenient therapeutic method to improve the dental implantation success rate and expand clinical implant indications

BDS Precise Point Positioning for Seismic Displacements Monitoring: Benefit from the High-Rate Satellite Clock Corrections

In order to satisfy the requirement of high-rate high-precision applications, 1 Hz BeiDou Navigation Satellite System (BDS) satellite clock corrections are generated based on precise orbit products, and the quality of the generated clock products is assessed by comparing with those from the other analysis centers. The comparisons show that the root mean square (RMS) of clock errors of geostationary Earth orbits (GEO) is about 0.63 ns, whereas those of inclined geosynchronous orbits (IGSO) and medium Earth orbits (MEO) are about 0.2–0.3 ns and 0.1 ns, respectively. Then, the 1 Hz clock products are used for BDS precise point positioning (PPP) to retrieve seismic displacements of the 2015 Mw 7.8 Gorkha, Nepal, earthquake. The derived seismic displacements from BDS PPP are consistent with those from the Global Positioning System (GPS) PPP, with RMS of 0.29, 0.38, and 1.08 cm in east, north, and vertical components, respectively. In addition, the BDS PPP solutions with different clock intervals of 1 s, 5 s, 30 s, and 300 s are processed and compared with each other. The results demonstrate that PPP with 300 s clock intervals is the worst and that with 1 s clock interval is the best. For the scenario of 5 s clock intervals, the precision of PPP solutions is almost the same to 1 s results. Considering the time consumption of clock estimates, we suggest that 5 s clock interval is competent for high-rate BDS solutions

Characterization of GNSS Signals Tracked by the iGMAS Network Considering Recent BDS-3 Satellites

The international GNSS monitoring and assessment system (iGMAS) tracking network has been established by China to track multi-GNSS satellites. A key feature of iGMAS stations is the capability to fully track new navigation signals from the recently deployed BDS-3 satellites. In addition to the B1I and B3I signals inherited from BDS-2 satellites, the BDS-3 satellites are capable of transmitting new open service signals, including B1C at 1575.42 MHz, B2a at 1176.45 MHz, and B2b at 1207.14 MHz. In this contribution, we present a comprehensive analysis and characterization of GNSS signals tracked by different receivers and antennas equipped in the iGMAS network, especially as they relate to BDS-3 signals. Signal characteristics are analyzed in terms of the carrier-to-noise density ratio for the different signals as measured by the receiver, as well as pseudo-range noise and multipath. Special attention is given to discussion of the satellite-induced code bias, which has been identified to exist in the code observations of BDS-2, and the inter-frequency clock bias (IFCB), which has been observed in the triple-frequency carrier phase combinations of GPS Block IIF and BDS-2 satellites. The results indicate that the satellite-induced code bias is negligible for all signals of BDS-3 satellites, while small IFCB variations with peak amplitudes of about 1 cm can be recognized in BDS-3 triple-carrier combinations