Molecular characterization of coxsackievirus B5 from the sputum of pneumonia children patients of Kunming, Southwest China.

BACKGROUND: CVB5 can cause respiratory infections. However, the molecular epidemiological information about CVB5 in respiratory tract samples is still limited. Here, we report five cases in which CVB5 was detected in sputum sample of pneumonia children patients from Kunming, Southwest China. METHODS: CVB5 isolates were obtained from sputum samples of patients with pneumonia. Whole-genome sequencing of CVB5 isolates was performed using segmented PCR, and phylogenetic, mutation and recombination analysis. The effect of mutations in the VP1 protein on hydration were analyzed by Protscale. The tertiary models of VP1 proteins were established by Colabfold, and the effect of mutations in VP1 protein on volume modifications and binding affinity were analyzed by Pymol software and PROVEAN. RESULTS: A total of five CVB5 complete genome sequences were obtained. No obvious homologous recombination signals comparing with other coxsackie B viruses were observed in the five isolates. Phylogenetic analysis showed that the five CVB5 sputum isolates were from an independent branch in genogroup E. Due to the mutation, the structure and spatial of the VP1 protein N-terminus have changed significantly. Comparing to the Faulkner (CVB5 prototype strain), PROVEAN revealed three deleterious substitutions: Y75F, N166T (KM35), T140I (KM41). The last two of the three deleterious substitutions significantly increased the hydrophobicity of the residues. CONCLUSIONS: We unexpectedly found five cases of CVB5 infection instead of rhinoviruses infection during our routine surveillance of rhinoviruses in respiratory tract samples. All five patients were hospitalized with pneumonia symptoms and were not tested for enterovirus during their hospitalization. This report suggests that enterovirus surveillance in patients with respiratory symptoms should be strengthened.

Development of a prognostic prediction model based on a combined multi-omics analysis of head and neck squamous cell carcinoma cell pyroptosis-related genes.

This study aimed to understand the prognosis of patients with head and neck squamous cell carcinoma (HNSCC) and to develop and validate a prognostic model for HNSCC based on pyroptosis-associated genes (PAGs) in nasopharyngeal carcinoma. The Cancer Genome Atlas database was used to identify differentially expressed PAGs. These genes were analyzed using the Kyoto Encyclopedia of Genes and Genomes functional annotation analyses and Gene Ontology analyses. The NLR family pyrin domain containing 1 (NLRP1) gene, charged multivesicular body protein 7 (CHMP7) gene, and cytochrome C (CYCS) gene were used to create a prognostic model for HNSCC. The results of the Kaplan-Meier (K-M) and Cox regression analyses indicated that the developed model served as an independent risk factor for HNSCC. According to the K-M analysis, the overall survival of high-risk patients was lower than that of low-risk patients. The hazard ratios corresponding to the risk scores determined using the multivariate and univariate Cox regression analyses were 1.646 (95% confidence interval (CI): 1.189-2.278) and 1.724 (95% CI: 1.294-2.298), respectively, and the area under the receiver operator characteristic curve was 0.621. The potential mechanisms associated with the functions of the identified genes were then identified, and the tumor microenvironment and levels of immune cell infiltration achieved were analyzed. The immune infiltration analysis revealed differences in the distribution of Th cells, tumor-infiltrating lymphocytes, regulatory T cells, follicular helper T cells, adipose-derived cells, interdigitating dendritic cells, CD8+ T cells, and B cells. However, validating bioinformatics analyses through biological experiments is still recommended. This study developed a prognostic model for HNSCC that included NLRP1, CHMP7, and CYCS.

Pulse compression of a single-frequency Q-switched fiber laser based on the cascaded four-wave mixing effect.

A pulse compressing technology of single-frequency Q-switched laser based on the cascaded four-wave mixing (CFWM) effect is demonstrated theoretically and experimentally, for the first time to the best of our knowledge. A theoretical model of the pulse compression is established through deconstructing the pulse duration evolution in the high-order Stokes and anti-Stokes lights of CFWM. A pulse compression ratio of (2|m|+1)1/2 is quantificationally obtained with m corresponding to the order number of the CFWM light. Utilizing dual-wavelength (DW) single-frequency Q-switched laser injected into a highly nonlinear fiber (HNLF), the pulse compression and the spectral broadening phenomenon are observed simultaneously. As the order number of the CFWM light increases from 0-order to 3-order, the pulse duration has reduced from 115 ns to 47 ns with a compression ratio of 2.45, which is essentially consistent with the theoretical analysis. The pulse compressing technique by CFWM is conducive to promoting the performance development of the single-frequency Q-switched laser, which can improve the system precision in the Lidar, trace gas detection, and high-precision ranging. Furthermore, this technology based on time-frequency transformation dynamics may be generally applicable to other single-frequency pulsed fiber lasers.

Quercetin targets VCAM1 to prevent diabetic cerebrovascular endothelial cell injury.

Introduction: Endothelial cells play important roles in neurodegenerative diseases caused by diabetes, therefore, we aimed at investigating the mechanisms through which endothelial cells are involved in diabetes development. Methods: Single cell analysis was performed to identify the major endothelial cell subtypes in cardiovascular tissues that are involved in diabetes development. A cell-cell communication approach was then used to identify ligand-receptor interaction pairs between these cell types. Differential expression analysis between the two experimental groups [standard chow diet group and diabetogenic diet with cholesterol (DDC) group] was used to identify diabetes-related differentially expressed genes (DEGs). The upregulated genes were used to identify candidate ligands or receptors, as well as the corresponding cell types. Cell trajectory inference was performed to identify the stage of cell development and changes in expression of candidate ligands or receptors during cell development. Gene set enrichment analysis (GSEA) was conducted to investigate the biological functions of genes of purpose. Finally, molecular dynamics simulations (MDSs) were used to predict potential drugs with the ability to target the proteins of purpose. Results: Seven cell types, including five endothelial cell subtypes (EC_1, EC_2, EC_3, EC_4, and EC_EndMT), were identified from endothelial cell-enriched single cell samples from the heart and aorta of mice. Cell-cell communication analysis revealed the potential ligand-receptor interactions between these cell types while five important ligand-receptor-associated genes, including Fn1, Vcam1, Fbn1, Col4a1, and Col4a2, were established by differential expression analysis. Among them, Vcam1 is mainly expressed in EC_EndMT and is involved in interactions between EC_EndMT and other cells. Cell trajectory extrapolation analysis revealed a shift from EC_2/EC_4 to EC_EndMT and a shift from EC_EndMT to EC_3/EC_1 during the progression of diabetes. GSEA analysis revealed that upregulation of VCAM1 may have inhibitory effects on cell growth and energy metabolism. Conclusion: EC_EndMT subtypes have a complex role in neurodegenerative diseases caused by diabetes. Through mechanisms involved in cell-cell communication, Vcam1 may play an important role in dysregulation of biological functions of EC_ EndMT. Molecular docking results of the quercetin-VCAM1 complex suggest that quercetin may be an effective drug for targeting this protein.

Based on Network Pharmacology and Molecular Dynamics Simulations, Baicalein, an Active Ingredient of Yiqi Qingre Ziyin Method, Potentially Protects Patients With Atrophic Rhinitis From Cognitive Impairment.

Cognition may be improved by the active ingredients of the Yiqi Qingre Ziyin method in patients with atrophic rhinitis (AR). This study aimed to identify potential targets of the Yiqi Qingre Ziyin method for the treatment of patients with cognitive impairment. Nasal mucosal tissue samples from patients with AR were subjected to proteomic assays, and differentially expressed proteins were obtained. To explore the mechanism of AR leading to mild cognitive impairment (MCI), a differential analysis of AR related differential proteins in the MCI related GSE140831 dataset was performed. Most AR-related differential proteins are also differentially expressed in peripheral blood tissues of MCI, have similar biological functions and are enriched in similar pathways. These co-expressed differential factors in AR and MCI are known as common differential proteins of AR and MCI (CDPAM). Based on the analysis and validation of the random forest, support vector machine and neural network models, CDPAM acted as a diagnostic marker for MCI risk. Cytochrome C (CYCS) was significantly upregulated in the peripheral blood of patients with MCI. The active ingredients in the Yiqi Qingre Ziqin method were obtained and targeted 137 proteins. Among these targeted proteins, CYCS belong to the CDPAM set. Molecular docking and molecular dynamics analysis revealed that baicalein, an active ingredient in the Yiqi Qingre Ziyin method, stably targeted the CYCS protein. Results of the enrichment analysis revealed that the up-regulation of CYCS expression may have a defensive effect on the cells to resist foreign stimuli. Therefore, baicalein, an active ingredient in the Yiqi Qingre Ziyin method, may prevent the development and progression of MCI by targeting the CYCS protein.

Exploring the Mechanism of Yiqi Qingre Ziyin Method in Regulating Neuropeptide Expression for the Treatment of Atrophic Rhinitis.

Atrophic rhinitis (AR) is a chronic disease that causes severe structural changes to the nasal mucosa leading to squamous epithelial metaplasia. However, treatment regarding AR remains a major challenge. We used network pharmacology and molecular docking methods to explore the potential mechanisms of the Yiqi Qingre Ziyin method to modulate neuropeptides in the treatment of AR. The active ingredients of the Yiqi Qingre Ziyin method and their targets of action were obtained from the Traditional Chinese Medicine Systematic Pharmacology Database Analysis Platform (TCMSP). Disease targets for AR were obtained from four databases: GeneCards, PharmGKB, DrugBank, and Online Mendelian Inheritance in Man (OMIM). A total of 59 active ingredients, 39 potential targets, and 76 relevant neuropeptides were obtained after deduplication. We constructed target interaction networks with the STRING database. Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed on the 14 potential target proteins. We used Cytoscape software to construct the "drug-active ingredient-potential target" and "ingredient-target-pathway" networks of the Yiqi Qingre Ziyin method for treating AR. Molecular docking results suggest that dipeptidyl peptidase 4 (DPP4), opioid receptor gene d1 (OPRD1), and opioid receptor m1 (OPRM1) are key targets for the Yiqi Qingre Ziyin method. Therefore, this study proposed a potential mechanism for the treatment of AR by affecting the expression of neuropeptide-related genes (including DPP4, OPRD1, and OPRM1), which may potentially improve the immune microenvironment of the nasal mucosa.

Molecular Characterization of the Viral Structural Genes of Human Rhinovirus A11 from Children Hospitalized with Lower Respiratory Tract Infection in Kunming.

BACKGROUND: The human rhinovirus (HRV) is a picornavirus that can cause a variety of respiratory diseases, including the aggravation of chronic respiratory diseases, such as bronchitis, pneumonia, and asthma. Although an increasing number of lower respiratory tract infection cases have been reported with HRV infection in Europe, few such cases have been reported in China. METHODS: The complete genomic sequences of the HRV-A11 epidemic strains were amplified and obtained by segmented polymerase chain reaction (PCR) and sequence, and then the phylogenetic, nucleotide mutation, recombinant, and comparative analyses of amino acid mutations were performed. RESULTS: Phylogenetic analyses showed that the epidemic strains from 3 rare cases of pneumonia belong to the HRV-A11 subgenotypes. All strains were highly similar to strains from the United States. No obvious homologous recombination signals were observed in the epidemic strains. There were 498 nucleotide and 47 amino acid mutations compared with the HRV-A11 prototype strain. Amino acid mutations were observed at the capsid protein region, P1a, RVA2147-2155, and RVA97-114 epitopes of these clinical strains. CONCLUSIONS: We reported the first case of HRV-A11-associated lower respiratory tract infection in China. These mutations in the P1a, HRV A-specific CD8, and CD4 T-cell epitopes might provide a reference for virological surveillance and vaccine development.

Bi(OTf)3-Catalyzed Alkyl-Intercepted Meyer-Schuster Rearrangement of Propargylic Alcohols for the Synthesis of 1,2,3,5-Tetrasubstituted Pentane-1,5-diones.

An alkyl intercepted Meyer-Schuster rearrangement reaction with α,ß-unsaturated ketones as the electrophiles was first investigated, which provided a facile method to construct 2-methylene-pentane-1,5-diones. Then the in situ generated 2-methylene-pentane-1,5-diones underwent a Michael addition to give diverse 2-malononitrile methyl substituted pentane-1,5-diones in a one-pot fashion. This transformation was reliable on a gram scale. The high yield, convenient experimental operation, and 100% atom economy made it a valuable method for the construction of 1,2,3,5-tetrasubstituted pentane-1,5-dione derivatives.

Structure of PDE3A-SLFN12 complex and structure-based design for a potent apoptosis inducer of tumor cells.

Molecular glues are a class of small molecular drugs that mediate protein-protein interactions, that induce either the degradation or stabilization of target protein. A structurally diverse group of chemicals, including 17-ß-estradiol (E2), anagrelide, nauclefine, and DNMDP, induces apoptosis by forming complexes with phosphodiesterase 3A (PDE3A) and Schlafen 12 protein (SLFN12). They do so by binding to the PDE3A enzymatic pocket that allows the compound-bound PDE3A to recruit and stabilize SLFN12, which in turn blocks protein translation, leading to apoptosis. In this work, we report the high-resolution cryo-electron microscopy structure of PDE3A-SLFN12 complexes isolated from cultured HeLa cells pre-treated with either anagrelide, or nauclefine, or DNMDP. The PDE3A-SLFN12 complexes exhibit a butterfly-like shape, forming a heterotetramer with these small molecules, which are packed in a shallow pocket in the catalytic domain of PDE3A. The resulting small molecule-modified interface binds to the short helix (E552-I558) of SLFN12 through hydrophobic interactions, thus "gluing" the two proteins together. Based on the complex structure, we designed and synthesized analogs of anagrelide, a known drug used for the treatment of thrombocytosis, to enhance their interactions with SLFN12, and achieved superior efficacy in inducing apoptosis in cultured cells as well as in tumor xenografts.

An integrative microenvironment approach for laryngeal carcinoma: the role of immune/methylation/autophagy signatures on disease clinical prognosis and single-cell genotypes.

The effects of methylation/autophagy-related genes (MARGs) and immune infiltration in the tumor microenvironment on the prognosis of laryngeal cancer were comprehensively explored in this study. Survival analysis screened out 126 MARGs and 10 immune cells potentially associated with the prognosis of laryngeal carcinoma. Cox and lasso regression analyses were then used to select 8 MARGs (CAPN10, DAPK2, MBTPS2, ST13, CFLAR, FADD, PEX14 and TSC2) and 2 immune cells (Eosinophil and Mast cell) to obtain the prognostic risk scoring system (pRS). The pRS was used to establish a risk prediction model for the prognosis of laryngeal cancer. The predictive ability of the prediction model was evaluated by GEO datasets and our clinical samples. Further analysis revealed that pRS is highly associated with single nucleotide polymorphism (SNP), copy number variation (CNV), immune checkpoint blockade (ICB) therapy and tumor microenvironment. Moreover, the screened pRS-related ceRNA network and circ_0002951/miR-548k/HAS2 pathway provide potential therapeutic targets and biomarkers of laryngocarcinoma. Based on the clustering results of pRS-related genes, single cells were then genotyped and revealed by integrated scRNA-seq in laryngeal cancer samples. Fibroblasts were found enriched in high risk cell clusters at the scRNA-seq level. Fibroblast-related ligand-receptor interactions were then exposed and a neural network-based deep learning model based on these pRS-related hub gene signatures was also established with a high accuracy in cell type prediction. In conclusion, the combination of single-cell and transcriptome laryngeal carcinoma landscape analyses can investigate the link between the tumor microenvironmental and prognostic characteristics.

Computer-aided discovery of phenylpyrazole based amides as potent S6K1 inhibitors.

Ribosomal protein S6 kinase beta-1 (S6K1) is an attractive therapeutic target. In this study, computational analysis of five thiophene urea-based S6K1 inhibitors was performed. Molecular docking showed that the five compounds formed hydrogen bonds with residues Glu173 and Leu175 of S6K1 and hydrophobic interactions with residues Val105, Leu97 and Met225, and these interactions were key elements for the inhibitory potency of the compounds. Binding free energy (ΔG bind) decomposition analysis showed that Leu97, Glu173, Val 105, Leu175, Leu97 and Met225 contribute the most to ΔG bind. Based on the computer results, phenylpyrazole based amides (D1-D3) were designed and synthesized. Biological evaluation revealed that D2 exhibited 15.9 nM S6K1 inhibition, medium microsomal stability and desirable bioavailability.

Improving Classification of Protein Interaction Articles Using Context Similarity-Based Feature Selection.

Protein interaction article classification is a text classification task in the biological domain to determine which articles describe protein-protein interactions. Since the feature space in text classification is high-dimensional, feature selection is widely used for reducing the dimensionality of features to speed up computation without sacrificing classification performance. Many existing feature selection methods are based on the statistical measure of document frequency and term frequency. One potential drawback of these methods is that they treat features separately. Hence, first we design a similarity measure between the context information to take word cooccurrences and phrase chunks around the features into account. Then we introduce the similarity of context information to the importance measure of the features to substitute the document and term frequency. Hence we propose new context similarity-based feature selection methods. Their performance is evaluated on two protein interaction article collections and compared against the frequency-based methods. The experimental results reveal that the context similarity-based methods perform better in terms of the F1 measure and the dimension reduction rate. Benefiting from the context information surrounding the features, the proposed methods can select distinctive features effectively for protein interaction article classification.

Superior laryngeal nerve loop: patterns and surgical implications.

This study clarifies the patterns of the superior laryngeal nerve loop (SLN loop), connecting the cervical sympathetic chain (CSC) and the SLN and its branches, so as to provide an anatomic basis for decreasing the risk of injury to the external laryngeal nerve (ELN) during neck surgery. Fifty Chinese adult human cadavers fixed with 4 % formalin were dissected, and their SLN loop patterns were analyzed and summarized. In 98 of 100 sides the CSC anastomosed with the SLN and its branches, forming a looped nerve structure which we called the SLN loop. The SLN loops could be divided into five types: e ( n ), t ( n ), i ( n ), t ( n ) e ( n ), and i ( n ) e ( n ) based on morphological variations. The results demonstrated that e ( n ) was most frequently found in the samples (82/100) followed by t ( n ) (9/100), i ( n ) (3/100), t ( n ) e ( n ) (2/100), and i ( n ) e ( n ) (2/100). Comparing with the previous work, we identified additional 18 subtypes of the SLN loop. The relations of the SLN loop to the surrounding structures were complicated, which brought more challenges to thyroidectomy. Thus, we do not advocate routine identification of ELN/ELN loop during the process of thyroidectomy, especially systematic identification of ELN during operation. However, this study introduces the possibility that nerve injury can be avoided by exposure of the nerve via careful dissection in the region of the superior pole of the thyroid gland to the extent that we can initiate individual ligation of the superior polar vessels, along with the help of neuromonitors, video monitors, and magnifying loupes.

An applied anatomical study on the recurrent laryngeal nerve and inferior thyroid artery.

PURPOSE: The aim of this study was to provide some important information about the morphology and topography of the recurrent laryngeal nerve (RLN) and inferior thyroid artery (ITA), which significantly helps localize and protect the RLN in neck surgery, especially in thyroid surgery. METHODS: Eighty adult cadavers (160 sides) fixed with formalin were dissected, analyzed and measured. RESULTS: (1) 87.5% of the RLNs gave off multiple branches like a tree; the incidence of the RLN loop, connecting one branch to another was 3.125%; in 9.375%, one branch of RLN combined with cervical sympathetic chain (CSC) or superior laryngeal nerve (SLN). (2) A double RLN appeared in four sides, a non-recurrent inferior laryngeal nerve appeared in two cases. (3) In two cases, the RLN communicated with both of the SLN and the CSC near thyroid gland. (4) Most of the ITAs was derived from thyrocervical trunk, and divided into two or three branches before entering the thyroid gland. (5) Three ITAs gave off esophageal branch, one ITA gave off tracheal branch, one right ITA originated abnormally. (6) On the left side, the RLN was behind the ITA in 86.25% of the cases, in front of the artery in 7.5%, the nerve was between artery branches in 2.5%, the artery was between nerve branches in 1.25%, and was among the combined in 2.5%. On the right side, the RLN was in front of the artery in 75.0%, behind the artery in 10.0%, among the branches of the artery in 5.0%, 10.0% the branches of both nerves and artery were interlaced that the relationship between the branches of the nerve and the artery was uncertain. CONCLUSIONS: Because of the variability of the RLN and ITA and the complicated relationship between them, it is necessary to dissect and recognize the RLN to avoid mistaking, ignoring, and misligating of the nerve before ligating the ITA.

Scanning white-light interferometer for measurement of the thickness of a transparent oil film on water.

The thickness of a transparent layer of oil upon the surface of water is measured as the distance between the surface of oil film and the interface of the oil with the water. Two experimental results have demonstrated that the interface can reflect a white-light beam well enough to form an interferogram, even if the light is subjected to oil-film dispersion. When a beam of white light is incident vertically onto the oil-film surface, a scanning white-light interferometer in the Michelson configuration is employed to locate two serial reflections, surface reflection and interface reflection. The thickness of the transparent oil film on water is calculated based on the separation of these two interferograms. A limitation thickness, approximately 250 microm with 1.25 microm resolution, is achieved under the condition that there is 50 nW of optical power incident onto the oil-film surface with a wavelength centered at 1310 nm.