Data driven methods have gained momentum in recent years in solving highly non-linear engineering problems that are challenging to solve using conventional methods. In this paper, we present a hybrid ...neural network model to predict the lateral response of large-diameter monopiles in multi-layered soil. The hybrid neural network consists of a mixture of convolutional and fully-connected layers, which capture the impacts of the soil profile, the pile geometry, and loading conditions on the lateral load response of monopiles. To train the neural network model, we produced data from high-fidelity three-dimensional (3D) finite element (FE) models that are validated against full-scale pile load tests. To ensure consistent model performance across the entire range of pile capacities considered in the dataset (ranging from approximately 100 kN to 100,000 kN), we utilize the relative error (percentage error) as the criterion for training the model. To achieve this goal, we explored six different combinations of data transformation methods (i.e., natural logarithm and root transformations) and cost functions. Among these models, the model trained with Mean Squared Error (MSE) using natural logarithm transformation yielded the most accurate and consistent predictions of the lateral capacities of monopiles. To demonstrate the strengths of the developed neural network model, it was used as a surrogate model to perform pile design optimization using sequential quadratic programming. In addition, a design example is provided to show how the developed method can be easily implemented.
Colorectal cancer (CRC) liver metastasis accounts for the majority of fatalities associated with CRC. Early detection of metastasis is crucial for improving patient outcomes but can be delayed due to ...a lack of symptoms. In this research, we aimed to investigate CRC metastasis-related biomarkers by employing a machine learning (ML) approach and experimental validation. The gene expression profile of CRC patients with liver metastasis was obtained using the GSE41568 dataset, and the differentially expressed genes between primary and metastatic samples were screened. Subsequently, we carried out feature selection to identify the most relevant DEGs using LASSO and Penalized-SVM methods. DEGs commonly selected by these methods were selected for further analysis. Finally, the experimental validation was done through qRT-PCR. 11 genes were commonly selected by LASSO and P-SVM algorithms, among which seven had prognostic value in colorectal cancer. It was found that the expression of the MMP3 gene decreases in stage IV of colorectal cancer compared to other stages (P value < 0.01). Also, the expression level of the WNT11 gene was observed to increase significantly in this stage (P value < 0.001). It was also found that the expression of WNT5a, TNFSF11, and MMP3 is significantly lower, and the expression level of WNT11 is significantly higher in liver metastasis samples compared to primary tumors. In summary, this study has identified a set of potential biomarkers for CRC metastasis using ML algorithms. The findings of this research may provide new insights into identifying biomarkers for CRC metastasis and may potentially lay the groundwork for innovative therapeutic strategies for treatment of this disease.
Objective. Oral tongue squamous cell carcinoma (OTSCC) and buccal squamous cell carcinoma (BSCC) are the first and second leading causes of oral cancer, respectively. OTSCC and BSCC are associated ...with poor prognosis in patients with oral cancer. Thus, we aimed to indicate signaling pathways, Gene Ontology terms, and prognostic markers mediating the malignant transformation of the normal oral tissue to OTSCC and BSCC. Methods. The dataset GSE168227 was downloaded and reanalyzed from the GEO database. Orthogonal partial least square (OPLS) analysis identified common differentially expressed miRNAs (DEMs) in OTSCC and BSCC compared to their adjacent normal mucosa. Next, validated targets of DEMs were identified using the TarBase web server. With the use of the STRING database, a protein interaction map (PIM) was created. Using the Cytoscape program, hub genes and clusters within the PIM were shown. Next, gene-set enrichment analysis was carried out using the g:Profiler tool. Using the GEPIA2 web tool, analyses of gene expression and survival analysis were also performed. Results. Two DEMs, including has-miR-136 and has-miR-377, were common in OTSCC and BSCC (p value <0.01; |Log2 FC| > 1). A total of 976 targets were indicated for common DEMs. PIM included 96 hubs, and the upregulation of EIF2S1, CAV1, RAN, ANXA5, CYCS, CFL1, MYC, HSP90AA1, PKM, and HSPA5 was significantly associated with a poor prognosis in the head and neck squamous cell carcinoma (HNSCC), while NTRK2, HNRNPH1, DDX17, and WDR82 overexpression was significantly linked to favorable prognosis in the patients with HNSCC. “Clathrin-mediated endocytosis” was considerably dysregulated in OTSCC and BSCC. Conclusion. The present study suggests that has-miR-136 and has-miR-377 are underexpressed in OTSCC and BSCC than in normal oral mucosa. Moreover, EIF2S1, CAV1, RAN, ANXA5, CYCS, CFL1, MYC, HSP90AA1, PKM, HSPA5, NTRK2, HNRNPH1, DDX17, and WDR82 demonstrated prognostic markers in HNSCC. These findings may benefit the prognosis and management of individuals with OTSCC/BSCC. However, additional experimental verification is required.
Background. Mitogen-activated protein kinase 3 (MAPK3) mediates the onset, progression, metastasis, drug resistance, and poor prognosis in various malignancies, including glioma, liver, ovarian, ...thyroid, lung, breast, gastric, and oral cancers. Negative regulation of MAPK3 expression using miRNAs has led to therapeutic effects in cancer. Objectives. The present study performed molecular docking and dynamics simulation to identify potential MAPK3 inhibitors from natural flavonoids, possibly leading to drug development in cancer therapy. Methods. A computational drug discovery approach was performed using the AutoDock tool to identify potential MAPK3 inhibitors from 46 plant-based flavonoids. A cross-validation study was executed using the Schrödinger Maestro docking tool. Molecular dynamics (MD) was executed to evaluate the stability of docked poses between the top-ranked compounds and the MAPK3 catalytic domain. Interactions among the most potent MAPK3 inhibitors and residues within the receptor’s active site were studied using the BIOVIA Discovery Studio Visualizer before and after 100 ns MD simulations. Results. Kaempferol 3-rutinoside-4′-glucoside, kaempferol 3-rutinoside-7-sophoroside, rutin, and vicenin-2 exhibited a magnificent binding affinity to the receptor’s active site. In addition, the stability of the docked poses of these compounds seemed to be stable after ∼45 ns computer simulations. Conclusion. The present study suggests that kaempferol 3-rutinoside-4′-glucoside, kaempferol 3-rutinoside-7-sophoroside, rutin, and vicenin-2 could strongly bind to the MAPK3 catalytic site and could be assigned as a potent inhibitor for MAPK3. These findings may be helpful in the treatment of various cancers. However, further validation experiments are needed.
Objective. Ameloblastoma is a benign odontogenic tumor that may lead to ameloblastic carcinoma. This study aimed to determine potential signaling pathways and biological processes, critical genes and ...their regulating transcription factors (TFs), and miRNAs, as well as protein kinases involved in the etiology of primary ameloblastoma. Methods. The dataset GSE132472 was obtained from the GEO database, and multivariate statistical analyses were applied to identify differentially expressed genes (DEGs) in primary ameloblastoma tissues compared to the corresponding normal gingiva samples. A protein-protein interaction (PPI) map was built using the STRING database. The Cytoscape software identified significant modules and the hub genes within the PPI network. Gene Ontology annotation and signaling pathway analyses were executed by employing the DAVID and Reactome databases, respectively. Significant TFs and miRNAs acting on the hub genes were identified using the iRegulon plugin and MiRWalk 2.0 database, respectively. A protein kinase enrichment analysis was conducted using the online Kinase Enrichment Analysis 2 (KEA2) web server. The approved drugs acting on the hub genes were also found. Results. A total of 1,629 genes were differentially expressed in primary ameloblastoma (P value <0.01 and |Log2FC| > 1). HRAS, CDK1, MAPK3, ERBB2, COL1A1, CYCS, and BRCA1 demonstrated high degree and betweenness centralities in the PPI network. E2F4 was the most significant TF acting on the hub genes. BTK was the protein kinase significantly enriched by the TFs. Cholesterol biosynthesis was considerably involved in primary ameloblastoma. Conclusions. This study provides an intuition into the potential mechanisms involved in the etiology of ameloblastoma.
Objective. MAPK3 activates several nuclear transcription factors, including c-Jun and c-fos, by phosphorylating its downstream cytoplasmic protein, thereby contributing to cell proliferation and ...survival. Different carcinomas’ initiation, progression, cancer cell metastasis, and drug resistance have been associated with MAPK3 overexpression. Given the need for new and potent MAPK3 inhibitors, this study aimed to explore the potential of anthraquinones (AQs) as organic compounds capable of inhibiting MAPK3. Methods. Using AutoDock 4.0 software, the binding affinity of 21 AQs to the receptor’s active site was evaluated. AQs were ranked based on their ΔGbinding values to the receptor’s active site, with the highest rankings receiving the most favorable scores. The Discovery Studio Visualizer tool was used to demonstrate the interaction modes between the highest-ranked AQs and the MAPK3 catalytic site. Furthermore, a 100-nanosecond molecular dynamics (MD) computer simulation was performed to assess the stability of the docked pose of the most potent enzyme inhibitor identified in this study. Results. The binding affinity of emodin-8-glucoside, aloe-emodin 8-glucoside, pulmatin, rhodoptilometrin, and hypericin to the receptor’s ATP binding cleft was noteworthy, as the ΔGbinding values were < −10 kcal/mol. In addition, emodin-8-glucoside, aloe-emodin 8-glucoside, and pulmatin were found to have inhibition constant values at the picomolar concentration. According to our computer simulation results, the docked pose of emodin-8-glucoside within the active site of MAPK3 achieved a stable state after 70 ns. In other words, the root mean square deviation (RMSD) graph indicated stability within the 70–100 ns timeframe. Conclusion. Inhibition of MAPK3 by emodin-8-glucoside, aloe-emodin 8-glucoside, pulmatin, rhodoptilometrin, and hypericin may have therapeutic potential in cancer treatment.
Staphylococcus aureus (S. aureus) is responsible for several disorders including skin and soft tissue infections, bacteremia, pulmonary infections, septic arthritis, osteomyelitis, meningitis, ...gastroenteritis, toxic-shock syndrome, and urinary tract infections. Methicillin-resistant S. aureus (MRSA) contains penicillin-binding protein 2a (SauPBP2a) responsible for catalyzing the peptidoglycan production within the bacterial cell wall. The binding affinity of SauPBP2a to beta-lactam antibiotics is low, and thus, it is necessary to discover new effective SauPBP2a inhibitors to combat mortality and morbidity in patients affected by MRSA. The binding affinity of 46 natural flavonoids to the SauPBP2a active site was examined via molecular docking analysis. The stability of docked poses associated with the top-ranked flavonoids was tested by performing molecular dynamics (MD) in 10 nanoseconds (ns) computer simulations. Kaempferol 3-rutinoside-7-sophoroside and rutin demonstrated a considerable binding affinity to the SauPBP2a active site (ΔGbinding < −11 kcal/mol). Their docked poses were found to be stable for 10 ns MD simulations. Kaempferol 3-rutinoside-7-sophoroside and rutin also exhibited salient binding affinity to the enzyme’s allosteric site. This study suggests that kaempferol 3-rutinoside-7-sophoroside and rutin may be considered as drug candidates for therapeutic aims in several human infections associated with MRSA. Nevertheless, in vitro and in vivo confirmations are warranted.
Background: Tooth decay (TD) is a multifactorial disorder, and several factors are involved in its etiology. Objective: The present study aimed to unravel the main genes and molecular mechanisms ...underlying TD. Methods: The dataset GSE1629 in the Gene Expression Omnibus (GEO) database was analyzed to uncover differentially expressed genes (DEGs) in patients with TD compared to patients with sound teeth. A protein-protein interaction network was built, and the most important clusters, hub genes, transcription factors (TFs), and protein kinases involved in the regulation of TFs were disclosed. Signaling pathways and Gene Ontology terms dysregulated in TD were also identified. Results: A total of 196 DEGs were determined (false discovery rate<0.001; |Log2 fold change|>1). PTPRC, ITGB2, TYROBP, MMP9, CXCL8, CD44, CCL2, C1QB, C3, and SPP1 were considered hub genes. Further, BPTF and MAPK1 were demonstrated to be the highest TFs and protein kinases likely involved in the pathogenesis of TD, respectively. Conclusion: PTPRC, ITGB2, TYROBP, MMP9, CXCL8, CD44, CCL2, C1QB, C3, SPP1, BPTF, and MAPK1 may be regarded as potential markers for the therapeutic purposes of TD.
Chronic Kidney Disease (CKD) is a global health problem annually affecting millions of people around the world. It is a comprehensive syndrome, and various factors may contribute to its occurrence. ...In this study, it was attempted to provide an accurate definition of chronic kidney disease; followed by focusing and discussing on molecular pathogenesis, novel diagnosis approaches based on biomarkers, recent effective antigens and new therapeutic procedures related to high-risk chronic kidney disease such as membranous glomerulonephritis, focal segmental glomerulosclerosis, and IgA nephropathy, which may lead to end-stage renal diseases. Additionally, a considerable number of metabolites and proteins that have previously been discovered and recommended as potential biomarkers of various CKD
using '-omics-' technologies, proteomics, and metabolomics were reviewed.
BackgroundHuman carbonic anhydrases (CAs) play a role in various pathological mechanisms by controlling intracellular and extracellular pH balance. Irregular expression and function of CAs have been ...associated with multiple human diseases, such as obesity, cancer, glaucoma, and epilepsy. In this work, we identify herbal compounds that are potential inhibitors of CA VI. MethodsWe used the AutoDock tool to evaluate binding affinity between the CA VI active site and 79 metabolites derived from flavonoids, anthraquinones, or cinnamic acids. Compounds ranked at the top were chosen for molecular dynamics (MD) simulations. Interactions between the best CA VI inhibitors and residues within the CA VI active site were examined before and after MD analysis. Additionally, the effects of the most potent CA VI inhibitor on cell viability were ascertained in vitro through the 2,5-diphenyl-2H-tetrazolium bromide (MTT) assay. ResultsKaempferol 3-rutinoside-4-glucoside, orientin, kaempferol 3-rutinoside-7-sophoroside, cynarin, and chlorogenic acid were estimated to establish binding with the CA VI catalytic domain at the picomolar scale. The range of root mean square deviations for CA VI complexes with kaempferol 3-rutinoside-4-glucoside, aloe-emodin 8-glucoside, and cynarin was 1.37 to 2.05, 1.25 to 1.85, and 1.07 to 1.54 Å, respectively. The MTT assay results demonstrated that cynarin had a substantial effect on HCT-116 cell viability. ConclusionThis study identified several herbal compounds that could be potential drug candidates for inhibiting CA VI.
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