A metabolic map and artificial intelligence-aided identification of nasopharyngeal carcinoma via a single-cell Raman platform.

BACKGROUND: Nasopharyngeal carcinoma (NPC) is a complex cancer influenced by various factors. This study explores the use of single-cell Raman spectroscopy as a potential diagnostic tool for investigating biomolecular changes associated with NPC carcinogenesis. METHODS: Seven NPC cell lines, one immortalised nasopharyngeal epithelial cell line, six nasopharyngeal mucosa tissues and seven NPC tissue samples were analysed by performing confocal Raman spectroscopic measurements and imaging. The single-cell Raman spectral dataset was used to quantify relevant biomolecules and build machine learning classification models. Metabolomic profiles were investigated using ultra-performance liquid chromatography-tandem mass spectrometer (UPLC-MS/MS). RESULTS: By generating a metabolic map of seven NPC cell lines, we identified an interplay of altered metabolic processes involving nucleic acids, amino acids, lipids and sugars. The results from spatially resolved Raman maps and UPLC-MS/MS metabolomics were consistent, revealing an increase of unsaturated fatty acids in cancer cells, particularly in highly metastatic 5-8F and poorly differentiated CNE2 cells. The classification model achieved a nearly perfect classification when identifying NPC and non-NPC cells with an ROC-AUC of 0.99 and a value of 0.97 when identifying 13 tissue samples. CONCLUSION: This study unveils a complex interplay of metabolic network and highlights the potential roles of unsaturated fatty acids in NPC progression and metastasis. This renders further research to provide deeper insights into NPC pathogenesis, identify new metabolic targets and improve the efficacy of targeted therapies in NPC. Artificial intelligence-aided analysis of single-cell Raman spectra has achieved high accuracies in the classification of both cancer cells and patient tissues, paving the way for a simple, less invasive and accurate diagnostic test.

Improving regional medical laboratory center report quality through a report recall management system.

OBJECTIVES: Currently, most medical laboratories do not have a dedicated software for managing report recalls, and relying on traditional manual methods or laboratory information system (LIS) to record recall data is no longer sufficient to meet the quality management requirements in the large regional laboratory center. The purpose of this article was to describe the research process and preliminary evaluation results of integrating the Medical Laboratory Electronic Record System (electronic record system) laboratory report recall function into the iLab intelligent management system for quality indicators (iLab system), and to introduce the workflow and methods of laboratory report recall management in our laboratory. METHODS: This study employed cluster analysis to extract commonly used recall reasons from laboratory report recall records in the electronic record system. The identified recall reasons were validated for their applicability through a survey questionnaire and then incorporated into the LIS for selecting recall reasons during report recall. The statistical functionality of the iLab system was utilized to investigate the proportion of reports using the selected recall reasons among the total number of reports, and to perform visual analysis of the recall data. Additionally, we employed P-Chart to establish quality targets and developed a "continuous improvement process" electronic flow form. RESULTS: The reasons for the recall of laboratory reports recorded in the electronic recording system were analyzed. After considering the opinions of medical laboratory personnel, a total of 12 recall reasons were identified, covering 73.05 % (1854/2538) of the recalled laboratory reports. After removing data of mass spectra lab with significant anomalies, the coverage rate increased to 82.66 % (1849/2237). The iLab system can generate six types of statistical graphs based on user needs, including statistical time, specialty labs (or divisions), test items, reviewers, reasons for report recalls, and distribution of the recall frequency of 0-24 h reports. The control upper limit of the recall rate of P-Chart based on laboratory reports can provide quality targets suitable for each professional group at the current stage. Setting the five stages of continuous process improvement reasonably and rigorously can effectively achieve the goal of quality enhancement. CONCLUSIONS: The enhanced iLab system enhances the intelligence and sustainable improvement capability of the recall management of laboratory reports, thus improving the efficiency of the recall management process and reducing the workload of laboratory personnel.

Blood Biomarkers Panels for Screening of Colorectal Cancer and Adenoma on a Machine Learning-Assisted Detection Platform.

OBJECTIVE: A mini-invasive and good-compliance program is critical to broaden colorectal cancer (CRC) screening and reduce CRC-related mortality. Blood testing combined with imaging examination has been proved to be feasible on screen for multicancer and guide intervention. The study aims to construct a machine learning-assisted detection platform with available multi-targets for CRC and colorectal adenoma (CRA) screening. METHODS: This was a retrospective study that the blood test data from 204 CRCs, 384 CRAs, and 229 healthy controls was extracted. The classified models were constructed with 4 machine learning (ML) algorithms including support vector machine (SVM), random forest (RF), decision tree (DT), and eXtreme Gradient Boosting (XGB) based on the candidate biomarkers. The importance index was used by SHapely Adaptive exPlanations (SHAP) analysis to identify the dominant characteristics. The performance of classified models was evaluated. The most dominating features from the proposed panel were developed by logistic regression (LR) for identification CRC from control. RESULTS: The candidate biomarkers consisted of 26 multi-targets panel including CEA, AFP, and so on. Among the 4 models, the SVM classifier for CRA yields the best predictive performance (the area under the receiver operating curve, AUC: .925, sensitivity: .904, and specificity: .771). As for CRC classification, the RF model with 26 candidate biomarkers provided the best predictive parameters (AUC: .941, sensitivity: .902, and specificity: .912). Compared with CEA and CA199, the predictive performance was significantly improved. The streamlined model with 6 biomarkers for CRC also obtained a good performance (AUC: .946, sensitivity: .885, and specificity: .913). CONCLUSIONS: The predictive models consisting of 26 multi-targets panel would be used as a non-invasive, economical, and effective risk stratification platform, which was expected to be applied for auxiliary screening of CRA and CRC in clinical practice.

The Comparison of Biomolecular Changes of Epstein-Barr Virus Infection in Nasopharyngeal Epithelial Cells Using Confocal Raman Microspectroscopy.

BACKGROUND: Due to its unique fingerprinting properties, Confocal Raman microscopy (CRM) can be used to examine the biomolecular changes of viruses invading and manipulating host cells. Recently, the biochemical changes due to the invasion and infection of B lymphocyte cells, nerve cells, and epithelial cells by Epstein-Barr virus (EBV) have been reported. However, biomolecular changes in nasopharyngeal epithelial cells that result from EBV infection are still poorly understood. METHODS: In continuation of our prior investigation of EBV infection in nasopharyngeal epithelial cells, we tried to expound on biomolecular changes in EBV-infected nasopharyngeal epithelial cells using Raman microspectroscopy. EBV has two life cycles, latent infection and lytic replication. We have established latent and lytic infection models at the cellular level. In order to understand the characteristics of the two patterns of EBV infection, we used Raman spectroscopy to identify the changes in biomolecules of EBV latent cells (CNE2, CNE2-EBV) and lytic cells (NPEC1-BMI1-CN, NPEC1-BMI1-EBV). RESULTS: During latent infection, levels of glycogen, protein, and lipid molecules in the cell increased while levels of nucleic acid and collagen molecules decreased. Molecular levels of glycogen, proteins, and nucleic acids are reduced during lytic infection. We found that molecular levels of nucleic acid decreased during two different periods of infection, whereas levels of other biomolecules showed the opposite trend. Glycogen, proteins, lipids, nucleic acids, and other molecules are associated with alterations in cellular biochemical homeostasis. These changes correspond to unique Raman spectra in infected and uninfected cells associated with specific biomolecules that have been proven. These molecules are mainly responsible for cellular processes such as cell proliferation and apoptosis. The Raman signatures of these biomolecular changes depend on the different phases of viral infection. CONCLUSIONS: Therefore, by using CRM, it is possible to discern details in the progression of EBV infection in nasopharyngeal epithelial cells at the molecular level.

Upregulated CD8+ MAIT cell differentiation and KLRD1 gene expression after inactivated SARS-CoV-2 vaccination identified by single-cell sequencing.

Background: The primary strategy for reducing the incidence of COVID-19 is SARS-CoV-2 vaccination. Few studies have explored T cell subset differentiation and gene expressions induced by SARS-CoV-2 vaccines. Our study aimed to analyze T cell dynamics and transcriptome gene expression after inoculation with an inactivated SARS-CoV-2 vaccine by using single-cell sequencing. Methods: Single-cell sequencing was performed after peripheral blood mononuclear cells were extracted from three participants at four time points during the inactivated SARS-CoV-2 vaccination process. After library preparation, raw read data analysis, quality control, dimension reduction and clustering, single-cell T cell receptor (TCR) sequencing, TCR V(D)J sequencing, cell differentiation trajectory inference, differentially expressed genes, and pathway enrichment were analyzed to explore the characteristics and mechanisms of postvaccination immunodynamics. Results: Inactivated SARS-CoV-2 vaccination promoted T cell proliferation, TCR clone amplification, and TCR diversity. The proliferation and differentiation of CD8+ mucosal-associated invariant T (MAIT) cells were significantly upregulated, as were KLRD1 gene expression and the two pathways of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, and translational initiation. Conclusion: Upregulation of CD8+ MAIT cell differentiation and KLRD1 expression after inactivated SARS-CoV-2 vaccination was demonstrated by single-cell sequencing. We conclude that the inactivated SARS-CoV-2 vaccine elicits adaptive T cell immunity to enhance early immunity and rapid response to the targeted virus.

Relationship between carbon stock and the structure of coniferous and broad-leaved mixed forest in Tianmu Mountains, China.

Taking the coniferous and broad-leaved mixed forest of Tianmu Mountain National Nature Reserve in Zhejiang Province as research object, we divided the tree species into three pairs, including evergreen and deci-duous species, broad-leaved and coniferous species, dominant and non-dominant species, to compare the difference of the individual tree carbon stock of each pair and analyze the diameter distribution pattern and tree height distribution pattern of carbon stocks. The relationship between spatial structure and individual tree carbon stock was analyzed by using spatial structure indicators including V_Hegyi competition index, complete mingling and aggregation index, to reveal the relationship between the structure of coniferous and broad-leaved forests and carbon stocks, and provide a theoretical basis for management of forest carbon sequestration. The results showed that the average individual carbon stock for evergreen and deciduous species, broad-leaved and coniferous species, dominant and non-dominant species were 57.7 and 87.4 kg, 54.6 and 74.7 kg, 67.4 and 48.1 kg, respectively. The individual tree carbon stock of evergreen species was significantly lower than that of deciduous species, the individual tree carbon stock of broad-leaved species was significantly lower than that of coniferous species, and the individual tree carbon stock of dominant tree species was significantly higher than that of non-dominant tree species. The diameter distribution and height distribution of carbon stock of each species group obeyed normal distribution. The V_Hegyi competition index was significantly negatively correlated with individual tree carbon stock, and it was consistent with the power function distribution. Both complete mingling and aggregation index were linearly and positively correlated with individual tree carbon stock. The direction of influence of different spatial structures on the individual tree carbon stock was consistent. The structure of coniferous and broad-leaved mixed forest had a significant impact on individual tree carbon stock. In the management of forest carbon sequestration and sink enhancement, it is necessary to regulate the unreasonable forest structure and promote its succession to the climax community in order to improve forest carbon stock.

[Gravitational model-based competitive analysis of trees]. / 基于引力模型的林木竞争分析.

Whether the gravitational model can be used to analyze tree competition in forest community is a valuable question. A tree relative vitality circle based on the gravitational model can illustrate the magnitude of competitive tree vitality. A gravitational competition index based on the relative vitality circle of competitive trees can accurately depict the relationship between growth and competition. This study was conducted in the coniferous and broadleaf mixed forest of Tianmu Mountain National Nature Reserve in Zhejiang Province. We carried out correlation analyses between the V_Hegyi competition index and diameter at breast height (DBH), between the gravitational competition index and DBH, and between the two competition indices and the basal area increment. We further analyzed the correlation between the growth rate of DBH and the ratio of the two-phase gravitational competition index, that is, the ratio of the 2021 gravitational competition index to that of 2006. In addition, the correlation analysis was applied between the relative vitality circle diameter and DBH. We also compared the magnitudes of the competition indices between the living standing trees and the dead trees. The results showed that both competition indices were negatively correlated with DBH, and followed a power function relationship. The basal area increment was negatively correlated with each of the two competition indices. However, the gravitational competition index was better than V_Hegyi competition index for indicating the relationship between tree growth and tree competition. Compared with the ratio of the V_Hegyi competition indices, the ratio of the two-phase gravitational competition indices could better demonstrate the relationship between tree growth and tree competition. In the coniferous and broadleaved mixed forests, the correlation coefficient between the growth and competition of broadleaved species was greater than that of coniferous species. The dead trees were significantly influenced by competition. Tree relative vitality circle size was negatively correlated with DBH. The gravitational model was one of the critical models that reflect spatial interactions and could be applied to examine forest competition. The gravitational competition index could be used as a spatially structured indicator to evaluate tree competition and tree vitality, which could better indicate the relationship between tree growth and tree competition than the V_Hegyi competition index.

Aptamer-cocktail Functionalized Nano-microfluidic Chip for Enhancing Isolation and Characterization of Circulating Cancer Cells.

BACKGROUND/AIM: Circulating tumor cells (CTCs) have been shown to have a correlation to metastasis and prognosis of patients with cancer. The enumeration and downstream gene analysis of CTCs have attracted efforts for personalized medicine. However, enumeration and phenotypic profiling in most capture devices are challenging due to the rarity and heterogeneity of CTCs. Here, we report an aptamer-cocktail strategy coupled in nano-microfluidic chip for enhancing isolation performance and characterizing the phenotypes of CTCs. MATERIALS AND METHODS: Aptamer-cocktail recognizing EpCAM/Vimentin/EGFR/CD44 were bound to a nanopillar array on a nano-microfluidic chip. The recognition was validated with cancer cells by flow cytometry and the critical parameters were optimized with the nano-microfluidic chip. Finally, the system was applied to clinical samples. RESULTS: The proposed aptamer-cocktail showed the predominant affinity with MDA-MB-231 and SK-BR-3. When utilized to capture artificial clinical samples, it showed 71% to 83% capture efficiency. CTC detection rate was 100% in five pre-treatment and five post-treatment breast cancer patients. The enumeration data ranged from 6-33 per 2 ml. The number of CTCs in breast cancer patients before therapy was 1.27-2 times higher than that after therapy. CTCs with epithelial and mesenchymal phenotype were both detected and identified; interestingly, the mean diameter of CTCpck pos acquired in these cases was much larger than that of CTCvimentin pos Conclusion: The nano-microfluidic chip not only made it easier to phenotyping epithelial-like or mesenchymal-like CTCs, but can also be used to detect downstream genetic variation. The established platform can be applied in clinical research and facilitate auxiliary diagnosis with tumor recurrence and metastasis in advance.

Protective antigenic epitopes revealed by immunosignatures after three doses of inactivated SARS-CoV-2 vaccine.

Background: SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) has infected millions of people around the world. Vaccination is a pillar in the strategy to control transmission of the SARS-CoV-2 spread. Immune responses to vaccination require elucidation. Methods: The immune responses to vaccination with three doses of inactivated SARS-CoV-2 vaccine were followed in a cohort of 37 healthy adults (18-59 years old). Blood samples were collected at multiple time points and submitted to peptide array, machine learning modeling, and sequence alignment analyses, the results of which were used to generate vaccine-induced antibody-binding region (VIABR) immunosignatures (Registration number: ChiCTR2200058571). Results: Antibody spectrum signals showed vaccination stimulated antibody production. Sequence alignment analyses revealed that a third vaccine dose generated a new highly represented VIABR near the A570D mutation, and the whole process of inoculation enhanced the VIABR near the N501Y mutation. In addition, the antigen conformational epitopes varied between short- and long-term samples. The amino acids with the highest scores in the short-term samples were distributed primarily in the receptor binding domain (RBD) and N-terminal domain regions of spike (S) protein, while in the long-term samples (12 weeks after the 2nd dose), some new conformational epitopes (CEs) were localized to crevices within the head of the S protein trimer. Conclusion: Protective antigenic epitopes were revealed by immunosignatures after three doses of inactivated SARS-CoV-2 vaccine inoculation. A third dose results in a new top-10 VIABR near the A570D mutation site of S protein, and the whole process of inoculation enhanced the VIABR near the N501Y mutation, thus potentially providing protection from strains that have gained invasion and immune escape abilities through these mutation.

Longitudinal profile of neutralizing and binding antibodies in vaccinated and convalescent COVID-19 cohorts by chemiluminescent immunoassays.

INTRODUCTION: Surrogate rapid serological assay was urgently demanded for accessibly interpretation of immunity potency and duration of neutralizing antibody against SARS-CoV-2. The longitudinal trajectory of antibody profile with a reliable large-scale assay was crucial to judge the protective immune status, avoid futile therapy and provide insight into the booster vaccination minimizing the risk of COVID-19. METHODS: A total of 195 volunteers were enrolled for a two-doses procedure (0 and 28 days) of inactive vaccination, as well as ten COVID-19 convalescents. The serum was collected at six time point and detected by chemiluminescent immunoassay with SARS-CoV-2 neutralizing antibody (Nab), SARS-CoV-2 RBD immunoglobulin G (IgG) antibody (RBD IgG) and RBD total antibody. The diagnostic results and the correlation of antibody level were evaluated among three serological (Nab, RBD IgG, and RBD total antibody) assay, as well as with an authorized cPass kit (Nab). Referred to the assay-specific threshold, the seroconversion rate and dynamic titer of antibody were exhibited from 0 to 56 days since vaccination. RESULTS: There was no difference observed with diagnostic results between neutralizing and RBD IgG antibody (p > 0.05). Both diagnostic results of neutralizing and RBD IgG antibody testing differentiated from RBD total antibody assay (p < 0.05). The coefficient of correlation (R) was above 0.90 among the levels of those three antibodies, more than 0.60 in comparison with neutralizing antibody by cPass enzyme-linked immunoassay. The "S" varying pattern for various antibodies level was observed with time extension after vaccination. The seroconversion rate was below 11.1% in 2 weeks after the priming dose, while the value climbed to 81% in 1 week after the boosting dose. The seroconversion rate was maintained around 91%. The inactive vaccine elicited 81-fold higher antibody levels after finished the vaccination schedule than that at the basic point. Besides, the level of neutralizing antibody induced by vaccine was found with a 0.2-fold ratio by comparison with that in COVID-19 convalescents. CONCLUSION: The humoral immune response products including SARS-CoV-2 neutralizing, RBD IgG antibody and total antibody and the varying pattern of the antibody profile could be rapidly detected by CILA method. Meanwhile, the continuing and dynamic determination was attributed to evaluate the protection effect of humoral immunity against the SARS-CoV-2 infection.

Dynamic observation of SARS-CoV-2 IgM, IgG, and neutralizing antibodies in the development of population immunity through COVID-19 vaccination.

BACKGROUND: Currently, mass vaccine inoculation against coronavirus disease-2019 (COVID-19) has been being implemented globally. Rapid and the large-scale detection of serum neutralizing antibodies (NAbs) laid a foundation for assessing the immune response against SARS-CoV-2 infection and vaccine. Additional assessments include the duration of antibodies and the optimal time for a heightened immune response. METHODS: The performance of five surrogate NAbs-three chemiluminescent immunoassay (CLIA) and two enzyme-linked immunosorbent assays (ELISAs)-and specific IgM and IgG assays were compared using COVID-19-vaccinated serum (n = 164). Conventional virus neutralization test (cVNT) was used as a criterion and the diagnostic agreement and correlation of the five assays were evaluated. We studied the antibody responses after the two-dose vaccine in volunteers up to 6 months. RESULTS: The sensitivity and specificity of five surrogate NAb assays ranged from 84% to 100%. Our cVNT results indicated great consistency with the surrogate assays. At 28 days after primary vaccination, the seropositivities of the NAbs, IgG, and IgM were 6%, 4%, and 13%, respectively. After the booster dose, seropositivities reached 14%, 65%, and 97%, respectively. Six months after receipt of the second dose, the NAb positive rate was eventually maintained at 66%. In all COVID-19 convalescents, patients were detected with 100% NAb sat three months after discharge. CONCLUSION: COVID-19 vaccine induced a humoral immune response lasting at least six months. Rapid serological detection was used as a proxy for identifying changes in immunity levels and as a guide to whether an individual may require a booster vaccination.

Performance evaluation of an automatic chemiluminescence immune platform for SARS-CoV-2 neutralizing antibody after vaccination in real world.

OBJECTIVE: Reliable high-throughput serological assays for SARS-CoV-2 antibodies present an important role in the strength and duration of immunity after vaccination. The study investigated the analytical and clinical performances of neutralizing antibodies (NTAb) assay by chemiluminescent (CLIA), and SARS-CoV-2 neutralizing antibody after vaccination in real world. METHODS: The analytical performances of CLIA for SARS-CoV-2 NTAb were evaluated, followed by the sensitivity and specificity identified with a PRNT test from 50 volunteers. Then, a cohort of vaccine recipients (n = 37) were tracked with SARS-CoV-2 NTAb assay at prior to vaccination, one, three and six months post two doses. In real world, a total of 737 cases were recruited from physical examination center in Shenzhen Luohu People's Hospital (from Jun to August 2021) to analyze vaccination status. RESULTS: Serological assays on the CLIA were found with excellent characteristics including imprecision, repeatability and linearity. Besides, it was robust to icterus, lipemia and hemolysis. The good sensitivity and specificity were obtained at 98% and 100%, respectively. NTAb results showed a high correlation with PRNT50 titers (r 0.61). Until July 2021, the BBIBP-CorV (76.3%) and Sinovac CoronaVac (20.5%) were the predominant vaccines injection in Shenzhen, China. Adolescent less than 18 years was the main unvaccinated group (52.1%). The seropositive rate of inactive SRAR-CoV-2 vaccines exceeded 97% after inoculation. The NTAb generated by Sinovac CoronaVac with the schedule of 0-56 days was found significantly lower than that by BBIBP-CorV (P < 0.001). The follow-up of NTAb changes in a cohort and the dynamic variation of NTAb in real world disclosed steep downward by almost three times for NTAb level occurred at three months post twice vaccinations. The seropositive ratio was at least 50% over 6 months. CONCLUSIONS: SARS-CoV-2 neutralizing antibodies assay show excellent analytical and clinical performances, and a high correlation with neutralizing activity. Anti-epidemic measures and the urgent trial of SARS-CoV-2 vaccine was calling for adolescents.

An aberrant DNA methylation signature for predicting the prognosis of head and neck squamous cell carcinoma.

Head and neck squamous cell carcinoma (HNSCC) is a common malignancy worldwide with a poor prognosis. DNA methylation is an epigenetic modification that plays a critical role in the etiology and pathogenesis of HNSCC. The current study aimed to develop a predictive methylation signature based on bioinformatics analysis to improve the prognosis and optimize therapeutic outcome in HNSCC. Clinical information and methylation sequencing data of patients with HNSCC were downloaded from The Cancer Genome Atlas database. The R package was used to identify differentially methylated genes (DMGs) between HNSCC and adjacent normal tissues. We identified 22 DMGs associated with 246 differentially methylated sites. Patients with HNSCC were classified into training and test groups. Cox regression analysis was used to build a risk score formula based on the five methylation sites (cg26428455, cg13754259, cg17421709, cg19229344, and cg11668749) in the training group. The Kaplan-Meier survival curves showed that the overall survival (OS) rates were significantly different between the high- and low-risk groups sorted by the signature in the training group (median: 1.38 vs. 1.57 years, log-rank test, p < 0.001). The predictive power was then validated in the test group (median: 1.34 vs. 1.75 years, log-rank test, p < 0.001). The area under the receiver operating characteristic curve (area under the curve) based on the signature for predicting the 5-year survival rates, was 0.7 in the training and 0.73 in test groups, respectively. The results of multivariate Cox regression analysis showed that the riskscore (RS) signature based on the five methylation sites was an independent prognostic tool for OS prediction in patients. In addition, a predictive nomogram model that incorporated the RS signature and patient clinical information was developed. The innovative methylation signature-based model developed in our study represents a robust prognostic tool for guiding clinical therapy and predicting the OS in patients with HNSCC.

The Overexpression of NMHC IIA Promoted Invasion and Metastasis of Nasopharyngeal Carcinoma Cells.

Background: Nasopharyngeal carcinoma (NPC) is a kind of head and neck squamous cell carcinoma (HNSCC) with a strong tendency for metastasis and recurrence. Non-muscle myosin heavy chain IIA (NMHC IIA) plays important roles in recurrence and metastasis of cancers. However, the function and mechanism of NMHC IIA expression in NPC remain unclear. Methods: A receiver operating characteristic (ROC) curve was constructed for 141 specimens of HNSCC tissues and 44 control samples from The Cancer Genome Atlas (TCGA) database. Co-expressed genes with MYH9 were identified using LinkedOmics. Transcription factors (TFs) and miRNA regulation network were constructed using Networkanalyst. The migration and invasion ability of nasopharyngeal carcinoma cells were evaluated by in vitro migration and matrigel invasion assays, respectively. Results: The public microarray results showed that MYH9 expression levels were upregulated in HNSCC tissues compared with the matched adjacent normal tissues in this study (p<0.0001). The AUC of MYH9 reached up to 0.8303 at a cutoff value of 175.2, with a sensitivity and specificity of 70.21% and 86.36%, respectively. MYH9 expression was increased in lymph node metastasis HNSCC tumors compared with that in tumors without lymph node metastasis (p<0.05) and showed a strong positive association with expression of FLNA. High MYH9 and FLNA expression were related with poorer overall survival in HNSCC. MYH9 with positively associated genes regulated focal adhesion, cell-substrate junction assembly and cell morphogenesis were involved in differentiation using GO and KEGG analysis. MYH9 was correlated with a network of TFs including SP1, SRF, JUN and FOS in HNSCC. The suppression of endogenous NMHC IIA decreased cellular migration and invasion in HNE1 cells and reduced the expression of phosphorylation of EGFR, AKT and ERK. The over-expression of NMHC IIA increased cellular migration and invasion in COS-7 cells and increased the expression of phosphorylation of EGFR, AKT and ERK. Conclusion: Expression of NMHC IIA mRNA was higher in HNSCC than in the adjacent normal tissues. NMHC IIA expression was increased in lymph node metastasis HNSCC tumors compared with tumors without lymph node metastasis. High MYH9 was association with poorer overall survival in HNSCC. NMHC IIA expression increased the invasion and metastasis abilities of the nasopharyngeal cancer cell line in vitro by augmenting the expression of phosphorylation of EGFR, AKT and ERK. These findings will be beneficial for providing an effectively therapeutic strategy for NPC.

Magnetic particles encoding a suspension probe for ultra-sensitive and quantitative determination of atrazine.

As a highly toxic and widely used herbicide, atrazine poses a serious threat to food safety as well as overall environmental and human health. Due to complex matrix interference and the difficulty of signal enrichment, there is an urgent need for a convenient, fast, and ultrasensitive method that detects trace atrazine without concern for matrix effects. Here, we provide the first account of a sensitive and rapid suspension probe based on magnetic microspheres used to detect atrazine in herbs. The self-made magnetic beads featured -COOH groups and were used as the carrier to construct immunofluorescent probes. These probes then conjugated with the atrazine antigen through an activated ester method, ultimately binding to the antibody. Homogeneous detection was ensured using flow cytometry and the microflow optical channel along with allophycocyanin-conjugated goat-anti-mouse secondary antibody (APC-IgG-SecAb) as the fluorescent signal. The magnetic suspension probe allowed for high target enrichment and the inherent two-dimensional selective detection of flow cytometry effectively avoided any matrix interference. This method had good linearity across 1.69-23.19 ng mL-1. The IC50 and LOD values were 4.81 ng mL-1 and 0.95 ng mL-1, respectively; the sensitivity was increased three-fold relative to ELISA. After complete optimization, 2-N-morpholinoeth-anesulfonic acid was used as the coupling solution and maintained good mono-dispersity, stability, and reactivity for the labelled microspheres during the process. The entire experiment was simple, and effectively used reagents; moreover, both the labor required and detection time were greatly reduced. Critically, the strategy presented here greatly reduced interference from complex matrices, and saved preparation for matrix-matched solutions when different herbs were screened. Overall, this strategy was sensitive, rapid, eco-friendly, and labor-saving; collectively, these attributes make it well-suited for on-site screening of atrazine contamination and will allow for increased food safety.

Analytical performance evaluation of five RT-PCR kits for severe acute respiratory syndrome coronavirus 2.

BACKGROUND: We aimed to evaluate the analytical performance of five commercial RT-PCR kits (Genekey, Daan, BioGerm, Liferiver, and Yaneng) commonly used in China, since such comparison data are lacking. METHODS: A total of 20 COVID-19 confirmed patients and 30 negative nasopharyngeal swab specimens were analyzed by five kits. The detection ability of five RT-PCR kits was evaluated with 5 concentration gradients diluted by a single positive sample. The limit of detection was evaluated by N gene fragment solid standard. Two positive clinical specimens were used to evaluate the repeatability and imprecision. Finally, we used six human coronaviruses plasmid and four respiratory pathogens plasmid to check for cross-reactivity. RESULTS: The positive detection rate was 100% for Genekey, Daan, and BioGerm,and 90% for Liferiver and Yaneng in 20 clinical SARS-CoV-2 infection. The coincidence rate of five kits in 10 negative samples was 100%. The detection rate of target genes for Daan, BioGerm, Liferiver, and Yaneng was 100% from Level 1 to Level 3. In Level 4, only Daan detection rate was 100%. In Level 5, five kits presented poor positive rate. The limit of detection declared by each manufacturer was verified. The repeatability for target genes was less than 5% and so did the total imprecision. There is no cross-reactivity of five kits with six human coronaviruses and four respiratory pathogens for ORF1ab and N gene. CONCLUSIONS: Five RT-PCR kits assessed in this study showed acceptable analytical performance characteristics and are useful tools for the routine diagnosis of SARS-CoV-2.

Comparison of three automatic chemiluminescent immunoassays for monitoring dynamic profile of SARS-CoV-2 IgG and IgM.

BACKGROUND: Seldom performance evaluation and diagnosis comparison studies were reported for different chemiluminescent immunoassay (CLIA) kits approved under an emergency approval program for SARS-CoV-2 infection. METHODS: A total of 100 and 105 serum separately from non-infected populations and COVID-19 patients were detected with SARS-CoV-2 IgM and IgG kits. The characteristics including precision, functional sensitivity, linearity, and accuracy were evaluated for Axceed, iFlash, and Maglumi CLIA kits. RESULTS: Maglumi and iFlash had the best analytical sensitivity for IgM and IgG, respectively. Axceed kits had a linearity response in the detected concentration. The clinical sensitivity of Axceed, iFlash, and Maglumi was 68.0%, 64.9%, and 63.9% with a specificity of 99.0%, 96.0%, and 100% for IgM, 85.6%, 97.9%, and 94.8% with a specificity of 97.0% for IgG. ROC analysis indicated all kits had a diagnostic power greater than 0.9. Notably, either IgM or IgG kits obtained a poor agreement (Kappa value from 0.397 to 0.713) with others. Among 38 recovered patients, 94.7% had an effective immune response, and both seropositive IgM and IgG accounted for the biggest proportion (medium, 42 days onset), then followed by the single seropositive IgG (medium, 50 days onset) in Ab profile. CONCLUSION: The performance of CLIA kits satisfied the diagnosis of SARS-CoV-2 infection. Both positive of IgG and IgM contributes to improve the specificity, and a positive one will enhance the sensitivity.

Occurrence and analysis of mycotoxins in domestic Chinese herbal medicines.

For time immemorial, Chinese herbal medicines (CHMs) have been widely used in China for disease treatment and promotion of general well-being. However, in recent years, many studies have shown that mycotoxins produced by fungi could contaminate CHMs due to unfavourable pre- or post-harvest conditions, raising major concern for consumer safety. At present, there is a significant focus on developing novel mycotoxin detection methods for analysing CHMs, and numerous studies have aimed to determine which kinds of raw herbal materials are most susceptible to mycotoxin contamination. In this review, we focus on recent advances in understanding and detection of mycotoxins in domestic raw herbal materials and related products from 2000 to 2018. Aspects of mycotoxin contamination of CHMs covered in this review include common mycotoxin contaminants in CHMs, maximum mycotoxin residue limits, analytical methods for mycotoxin detection and their applications and limitations, as well as a brief discussion of the trends in ongoing research.

Consistency evaluation of Liferiver, Yaneng, Darui, and the Cobas 4800 test for high-risk human papillomavirus screening.

BACKGROUND: In recent years, several high-risk human papillomavirus (HR-HPV) tests have been developed. The assay capabilities need to be systematically reviewed. Here, we compared the clinical sample performance of three novel HR-HPV assays (Liferiver, Yaneng, and Darui) based on different platforms with the widely adopted cobas4800 test. METHODS: A total of 346 cervical swabs from women who were screened for cervical cancer were analyzed for the presence of 14 HR-HPV genotypes. The distinction between the four assays was investigated by the genotyping and direct sequencing. RESULTS: The positive rates of the four assays ranged from 61.56% to 64.16%. The overall concordance was 88.15%. The Yaneng assays displayed the best sensitivity (100%) and specificity (98.43%). The sensitivity (98.17%) and specificity (98.43%) of the Darui assay were superior to those of the cobas4800 test (97.72% and 93.70%, respectively). The Liferiver assay displayed comparable sensitivity with the cobas4800 test (95.89% and 97.72%, respectively). The specificity of the cobas4800 was lower than that of the Liferiver assay (93.70% vs. 97.64%). CONCLUSIONS: The three novel HR-HPV assays displayed good agreement with the cobas4800 test. The analytical performance of all four fulfilled the requirements of sensitivity and specificity for HR-HPV detection.

Development of a novel prognostic signature for predicting the overall survival of bladder cancer patients.

BACKGROUND: Bladder cancer is one of the most common malignancies. So far, no effective biomarker for bladder cancer prognosis has been identified. Aberrant DNA methylation is frequently observed in the bladder cancer and holds considerable promise as a biomarker for predicting the overall survival (OS) of patients. MATERIALS AND METHODS: We downloaded the DNA methylation and transcriptome data for bladder cancer from The Cancer Genome Atlas (TCGA), a public database, screened hypo-methylated and up-regulated genes, similarly, hyper-methylation with low expression genes, then retrieved the relevant methylation sites. Cox regression analysis was used to identify a nine-methylation site signature of a training group. Predictive ability was validated in a test group by receiver operating characteristic (ROC) analysis. RESULTS: We identified nine bladder cancer-specific methylation sites as potential prognostic biomarkers and established a risk score system based on the methylation site signature to evaluate the OS. The performance of the signature was accurate, with area under curve was 0.73 in the training group and 0.71 in the test group. Taking clinical features into consideration, we constructed a nomogram consisting of the nine-methylation site signature and patients' clinical variables, and found that the signature was an independent risk factor. CONCLUSIONS: Overall, the significant nine methylation sites could be novel prediction biomarkers, which could aid in treatment and also predict the overall survival likelihoods of bladder cancer patients.