Polymerase Chain Reaction Assay Research Articles

DEVELOPMENT OF A RAPID SNP PCR ASSAY TO DIFFERENTIATE BETWEEN EUROPEAN AND NORTH AMERICAN HAPLOTYPES OF ECHINOCOCCUS MULTILOCULARIS.

Herein we describe a single nucleotide polymorphism-specific polymerase chain reaction (PCR) assay to rapidly detect and differentiate variants belonging to the European and North American lineages of Echinococcus multilocularis in clinical samples. This is an extremely relevant and applicable test in North America because the range of E. multilocularis continues to expand across the continent and because of a rise in prevalence in wildlife, domestic animals, and humans. The endemic North American (NA) and introduced European (EU) variants are believed to have different pathogenic potentials, with the EU variants being more infective and pathogenic than the NA variants. The rise of the EU variants of E. multilocularis increases the risk of spillover from wildlife to humans because of its increased potential for infectivity. Current PCR-based diagnostics can detect E. multilocularis deoxyribonucleic acid (DNA), but DNA sequencing is required to identify the specific variant. Our assay provides a straightforward conventional PCR method to differentiate the NA and EU variants, and we suggest this same approach could be used for the diagnosis of other parasites or variants that are genetically very similar. As surveillance continues for E. multilocularis across North America, identifying the different genetic variants from different geographic regions will become essential to understanding the current epidemiological shift that the parasite is experiencing, as well as informing public health decisions in affected areas.

Esculin Alleviates Osteoarthritis Progression Through theSirt1/NF-κB Pathway.

Osteoarthritis (OA), a joint disease associated with inflammatory processes, contributes to joint destruction. Esculin (ESC) extracted from the stem bark of Fraxinus rhynchophylla Hance has been shown to possess anti-inflammatory properties. In this study, we investigated the effect of ESC on chondrocytes treated with IL-1β and its molecular mechanism. The importance and potential mechanism of ESC in the progression of OA were evaluated. The viability of chondrocytes after exposure to ESC was examined through the CCK-8 assays. The cells were then subjected to quantitative polymerase chain reaction (qPCR), western blot, and enzyme-linked immunosorbent assay (ELISA) techniques to analyze the degradation of the extracellular matrix (ECM) and occurrence of inflammation. The NF-κB mechanism was evaluated by western blot analysis, immunofluorescence (IF), and luciferase reporter assay. Molecular docking was performed to allow for predictions on proteins that interact with ESC. Moreover, the significance of Sirt1 was explored through a knockdown experiment based on siRNA. Micro-computed tomography (CT), H&E, Safranin O-Fast Green (S-O), and immunohistochemical analyses were carried out to assess the treatment efficacy of ESC on OA in destabilization of medial meniscus (DMM) models. ESC treatment effectively inhibited ECM degradation, modulated the levels of pro-inflammatory factors, and regulated the NF-κB signaling in chondrocytes exposed to IL-1β. Mechanistically, we found that ESCs bound to Sirt1 to inhibit the activity of the NF-κB mechanism. Furthermore, ESC treatment suppressed OA progression in the DMM models. Our findings reveal that ESC ameliorates OA progression via modulating the Sirt1/NF-κB axis. This demonstrates that ESC has the potential to be applied in the treatment of OA.

Serum MicroRNA-126-3p and Serum Vascular Endothelial Growth Factor for Vision Threatening Diabetic Retinopathy in Type 2 Diabetes Mellitus Patients

Purpose: To investigate the precise function of miRNA-126-3p in controlling the expression of the VEGF gene and the signalling cascade that it is linked to in patients with type 2 diabetes Mellitus (DM). Study Design: Cross-sectional analytical study. Place and Duration of Study: Prof Ngoerah General Hospital as a tertiary hospital in Bali, Indonesia from January-April 2022 Methods: This study involved 35 vision-threatening diabetic retinopathy (VTDR) and 30 non-VTDR patients of type 2 DM. After diagnosis of DR by vitreoretinal specialist, blood samples were drawn. Real-time polymerase chain reaction assays were performed to examine miRNA-126-3p and ELISA to detect VEGF. Continuous data were analyzed using median (minimum-maximum range) and categorical data were analyzed using percentages. The statistical analysis was conducted using SPSS for Windows version 25.0.Thedifference and relationship between the proportions were tested by the Chi-square test and logistic regression test. Results: In case group, there were 23 subjects (65.7%) with low serum miRNA-126-3p expression, while in the control group, there were 7 subjects (23.3%) with low serum miRNA-126-3p expression (OR=6.3; 95% CI 2.1-18.86). In the case group, 20 individuals (57.1%) had high serum VEGF levels of 71.6 ng/L, whereas in the control group, there were 6 individuals (20.0%) with high serum VEGF levels. There was a statistically significant difference between the two groups (OR=5.33; 95% CI 1.75-16.3). Conclusion: The miRNA-126-3p expression and serum VEGF levels are the risk factors for VTDR development in patients with type 2 diabetes.

Photobacterium damselae subsp. damselae in Stranded Cetaceans: A 6-Year Monitoring of the Ligurian Sea in Italy

Photobacterium damselae subsp. damselae (Pdd) is an increasingly common bacterium in post-mortem diagnostics of beached marine mammals, but little is known about its precise etiological responsibility. To estimate the prevalence of Pdd in stranded cetaceans from 2017 to 2022 on the Ligurian coast (Pelagos Sanctuary), we tested tissues from 53 stranded individuals belonging to four cetacean species. DNA extracts from cetacean tissue were screened using a polymerase chain reaction (PCR) assay targeting the Pdd ureC gene. Positive samples were screened by PCR for dly, hlyApl and hlyAch hemolysin genes, which were confirmed by sequencing. Twenty-two out of 53 (41.5%) cetaceans analyzed by PCR were confirmed for Pdd DNA in at least one tissue among those analyzed. Five of these cetaceans were positive for at least one of the hemolysin genes tested. In all Pdd-positive cetaceans, other pathogens that were considered responsible for the causa mortis of the animals were also found. The results provide new information on the spread of Pdd in cetaceans and support the thesis that Pdd might be an opportunistic agent that could contribute to worsening health conditions in subjects already compromised by other pathogens. However, further studies are needed to investigate and deepen this hypothesis.

Isolation and genetic characterization of canine adenovirus type 2 variant from raccoon dog (Nyctereutes procynoide koresis) in Republic of Korea

Canine adenovirus type 2 (CAV-2) is a common causative agent of respiratory disease in canines. There have been no reports of CAV-2 variants isolated from raccoon dogs. This study aims to investigate the biological and genetic characteristics of a novel Korean CAV-2 variant. Madin-Darby canine kidney cells were used to isolate the CAV-2 variant from 45 fecal swab samples. Diagnostic tools such as the cytopathic effect (CPE) assay, electron microscopy, polymerase chain reaction, and immunofluorescence and hemagglutination assays were used to confirm the presence of the CAV-2 isolate. A cross-virus neutralization assay was performed to verify the novelty of this CAV variant. Genetic analysis was performed using nucleotide sequences obtained through next-generation sequencing. The isolate was confirmed to be a CAV-2 variant based on the aforementioned methods and designated CAV2232. The number of bases in the fiber and E3 genes of CAV2232 were 1,626 and 414, respectively. Phylogenetic analysis of the fiber and E3 genes confirmed that CAV2232 was classified into a different clade from the known CAV-1 and CAV-2 strains. Mice inoculated with the CAV2232 vaccine developed high virus neutralization antibody titers of 1,024 (210) against CAV2232, while mice inoculated with CAV-1 and CAV-2 vaccines had low virus neutralization antibody titers of 12.9 (23.7) and 6.5 (22.7), respectively, against CAV2232. CAV2232 isolated from wild raccoon dog feces was classified as a novel CAV-2 variant. CAV2232 may therefore be used as an antigen for new vaccine development and serological investigations.

Comparison of Neurogenesis Promotion Effects between Cinnamoylquinic Acids in Neural Stem Cells from Adult Mice Brains.

Caffeoylquinic acids (CQAs) and feruloylquinic acids (FQAs), as cinnamoylquinic acids, have neurogenesis promotion effects. We studied for the first time the neurogenesis-enhancing effect of 3,4,5-tri-feruloylquinic acid (TFQA) compared to 3,4,5-tri-caffeoylquinic acid (TCQA), which has a similar structure, and explored their different cellular and molecular mechanisms in neural stem cells (NSCs) of mice brains. After 2 weeks of incubation, we first assessed the number and size of NSCs in TCQA and TFQA treatments. In NSCs treated for TCQA and TFQA, the NSC proliferation gene expression as well as neuronal and glial cell differentiation gene expressions improved. In the microarray assay, the erythroblastic oncogene B (ErbB) signaling pathway, as the common signaling of TCQA and TFQA treatments, was focused on and discussed. In our study, TCQA and TFQA treatments in NSCs showed a significant performance on improving synapse growth and neurogenesis compared with no treatment of NSCs. The two treatments in NSCs also had a significant activation of the ErbB signaling pathway, protein kinase B (AKT), and mitogen-activated protein kinase (MAPK) kinases. In particular, the TCQA-expressed proliferation gene myelocytomatosis oncogene (Myc) had the greatest connections significantly. TFQA treatment remarkably regulated the differentiation gene jun proto-oncogene (Jun), which was the gene with greatest direct relations, while Myc was also induced in TFQA treatment. In the overall quantitative real-time polymerase chain reaction (PCR) assay, TFQA had more outstanding neural proliferation and differentiation capabilities than TCQA in NSCs. Our study suggests that TFQA has greater therapeutic potential in neurogenesis promotion and neurodegenerative diseases compared with TCQA.

Development of a Multiplex Polymerase Chain Reaction Assay for Detecting Five Previously Unreported Papaya Viruses for Quarantine Purposes in Korea

There are concerns about the introduction and spread of plant pests and pathogens with globalization and climate change. As commercial control agents have not been developed for plant viruses, it is important to prevent virus spread. In this study, we developed a multiplex polymerase chain reaction (PCR) detection method to rapidly diagnose and control three DNA (papaya golden mosaic virus, Lindernia anagallis yellow vein virus, and melon chlorotic leaf curl virus) and two RNA (papaya leaf distortion mosaic virus and lettuce chlorosis virus) viruses that infect papaya. Specific primer sets were designed for the virus coat protein. Performing PCR, clear bands were observed with no non-specific reaction. Our multiplex PCR method can simultaneously detect small amounts of DNA/RNA to diagnose five viruses infecting papaya and prevent the spread of the virus.

Advancement and Challenges in Monitoring of CAR-T Cell Therapy: A Comprehensive Review of Parameters and Markers in Hematological Malignancies

Chimeric antigen receptor T-cell (CAR-T) therapy has revolutionized the treatment for relapsed/refractory B-cell lymphomas. Despite its success, this therapy is accompanied by a significant frequency of adverse events, including cytokine release syndrome (CRS), immune-effector-cell-associated neurotoxicity syndrome (ICANS), or cytopenias, reaching even up to 80% of patients following CAR-T cell therapy. CRS results from the uncontrolled overproduction of proinflammatory cytokines, which leads to symptoms such as fever, headache, hypoxia, or neurological complications. CAR-T cell detection is possible by the use of flow cytometry (FC) or quantitative polymerase chain reaction (qPCR) assays, the two primary techniques used for CAR-T evaluation in peripheral blood, bone marrow (BM), and cerebrospinal fluid (CSF). State-of-the-art imaging technologies play a crucial role in monitoring the distribution and persistence of CAR-T cells in clinical trials. Still, they can also be extended with the use of FC and digital PCR (dPCR). Monitoring the changes in cell populations during disease progression and treatment gives an important insight into how the response to CAR-T cell therapy develops on a cellular level. It can help improve the therapeutic design and optimize CAR-T cell therapy to make it more precise and personalized, which is crucial to overcoming the problem of tumor relapse.

Thoracic epithelioid inflammatory myofibroblastic sarcoma: a rare and aggressive disease with case report and literature review

Epithelioid inflammatory myofibroblastic sarcoma (EIMS) is a rare subtype of inflammatory myofibroblastic tumor, characterized to be an aggressive disease with high frequency of ALK rearrangement, rapid recurrence, and poor prognosis. Primary EIMS of thoracic origin is rarely observed. Herein, we described a case of 28-year-old female developed primary EIMS in the anterior mediastinum with hepatic metastasis. The EIMS displayed sheet-like growth of epithelioid and spindle cells with enlarged nuclei, abundant and eosinophilic cytoplasm, and infiltration of inflammatory cells. Immunohistochemical staining revealed positive expression of ALK in the nuclear membrane, and ALK rearrangement was identified by polymerase chain reaction assay. Alectinib showed partial response, and achieved a meaningful survival benefit for four months. Based on this case report and literature review, ALK inhibitor reveals promising activity on the rare but aggressive EIMS. Awareness of EIMS in thoracic disease and its clinicopathological features is essential to avoid erroneous diagnosis.

Thalidomide attenuates radiation-induced apoptosis and pro-inflammatory cytokine secretion in oral epithelial cells by promoting LZTS3 expression

Radiation-induced oral mucositis (RIOM) is a prevalent oral complication that occurs in individuals undergoing radiotherapy or radiation treatment for head and neck tumors. The presence of oral mucosal rupture and ulcerative lesions, which are the defining features of this condition, can significantly affect the quality of life of patients. Additionally, it can interfere with tumor therapy and contribute to an unfavorable prognosis. Current evidence suggests that cellular inflammation and programmed cell death are important factors in disease development. Moreover, thalidomide (THD) has been revealed to reduce the incidence and severity of RIOM in patients undergoing chemoradiotherapy for nasopharyngeal carcinoma. However, the mechanism through which THD improves RIOM remains unknown. This study aimed to investigate the role of LZTS3 in RIOM by analyzing various sequencing datasets and conducting knockdown and overexpression experiments. We used small interfering RNA transfection and LZTS3 overexpression, followed by validation through polymerase chain reaction, western blotting, flow cytometry, and enzyme-linked immunosorbent assay. In this study, we identified LZTS3 as a potential target for THD regulation in RIOM. Through a series of experiments, we confirmed that LZTS3 has the ability to inhibit the inflammatory response and apoptosis of cells. In addition, we also found that THD can regulate the expression of LZTS3 by upregulating, thereby affecting inflammatory response and apoptosis. We repeated these results in a live animal model. In summary, THD has the potential to reduce the occurrence of oral mucositis in patients by upregulating LZTS3 levels. These findings provide a promising avenue for future drug research and development to treat RIOM.

E74-like factor 4 promotes the proliferation, invasion, and migration of colorectal cancer cells via long non-coding RNA integrin subunit beta 8 antisense RNA 1-mediated histone H3 lysine 27 trimethylation modification.

Colorectal cancer (CRC) is a common malignancy in the gastrointestinal tract. The main objective of this study is to explore the potential mechanisms of E74-like factor 4 (ELF4) in CRC progression, providing a novel therapeutic target for CRC treatment. CRC cells and normal control cells were cultured. Levels of ELF4/long non-coding RNA integrin subunit beta 8 antisense RNA 1 (LncRNA ITGB8-AS1)/claudin-23 (CLDN23) were detected by real-time quantitative polymerase chain reaction or Western blot assay. ELF4 siRNA, ITGB8-AS1 pcDNA3.1, or CLDN23 siRNA were transfected into cells. Cell proliferation, migration, and invasion were evaluated. The enrichment of ELF4 on the ITGB8-AS1 promoter was detected. Dual-luciferase assay was employed to assess the binding between ELF4 and the ITGB8-AS1 promoter. RNA pull-down and RNA immunoprecipitation assays were conducted to investigate the binding between ITGB8-AS1 and enhancer of zeste homolog 2 (EZH2). The binding of EZH2 and histone H3 lysine 27 trimethylation (H3K27me3) to the CLDN23 promoter was detected. ELF4 and ITGB8-AS1 were upregulated in CRC cells, while CLDN23 was downregulated. Knockdown of ELF4 inhibited cell proliferation, invasion, and migration. Mechanistically, ELF4 transcriptionally activated ITGB8-AS1 and promoted the binding between ITGB8-AS1 and EZH2. EZH2 catalyzed H3K27me3 modification on the CLDN23 promoter, leading to decreased CLDN23 expression. Overexpression of ITGB8-AS1 or downregulation of CLDN23 could reduce the inhibitory effects of silencing ELF4 on CRC cell proliferation, migration, and invasion. ELF4 accelerates CRC progression through the ITGB8-AS1/CLDN23 axis, providing new therapeutic targets for CRC.

Molecular genotyping reveals multiple carbapenemase genes and unique blaOXA-51-like (oxaAb) alleles among clinically isolated Acinetobacter baumannii from a Philippine tertiary hospital

BackgroundAcinetobacter baumannii continued to be an important Gram-negative pathogen of concern in the clinical context. The resistance of this pathogen to carbapenems due to the production of carbapenemases is considered a global threat. Despite the efforts to track carbapenemase synthesis among A. baumannii in the Philippines, local data on its molecular features are very scarce. This study aims to characterize A. baumannii clinical isolates from a Philippine tertiary hospital through genotyping of the pathogen’s carbapenemase genes.MethodsAntibiotic susceptibility profiling, phenotypic testing of carbapenemase production, and polymerase chain reaction assays to detect the different classes of carbapenemase genes (class A blaKPC, class B blaNDM, blaIMP, blaVIM, and class D blaOXA-23-like, blaOXA-24/40-like, blaOXA-48-like, blaOXA-51-like, ISAba1-blaOXA-51-like, blaOXA-58-like) were performed in all collected A. baumannii, both carbapenem resistant and susceptible (n = 52).ResultsResults showed that the majority of the carbapenem-resistant strains phenotypically produced carbapenemases (up to 84% in carbapenem inactivation methods) and possessed the ISAba1-blaOXA-51-like gene complex (80%). Meanwhile, both carbapenem-resistant and carbapenem-susceptible isolates possessed multi-class carbapenemase genes including blaNDM (1.9%), blaVIM (3.9%), blaOXA-24/40-like (5.8%), blaOXA-58-like (5.8%), blaKPC (11.5%), and blaOXA-23-like (94.2%), which coexist with each other in some strains (17.3%). In terms of the intrinsic blaOXA-51-like (oxaAb) genes, 23 unique alleles were reported (blaOXA-1058 to blaOXA-1080), the majority of which are closely related to blaOXA-66. Isolates possessing these alleles showed varying carbapenem resistance profiles.ConclusionsIn summary, this study highlighted the importance of molecular genotyping in the characterization of A. baumannii by revealing the carbapenemase profiles of the pathogen (which may not be captured accurately in phenotypic tests), in identifying potent carriers of transferrable carbapenemase genes (which may not be expressed straightforwardly in antimicrobial susceptibility testing), and in monitoring unique pathogen epidemiology in the local clinical setting.

Association of COL4A2 indel polymorphism with the development of stomach adenocarcinoma in Chinese populations

Objective The objective of the study was to assess the potential association between the indel polymorphism (rs34802628) located within the intron of the collagen type ⅳ alpha 2 gene (COL4A2) and the susceptibility to stomach adenocarcinoma (STAD) within a Chinese population. Methods Peripheral venous blood samples were collected from a total of 497 STAD patients and 804 healthy control individuals to extract genomic DNA. The genotyping of the COL4A2 rs34802628 polymorphism was carried out using a polymerase chain reaction assay. Additionally, statistical analyses were conducted on the expression levels of COL4A2 mRNA using the GEPIA database. Meanwhile, the expression of COL4A2 mRNA was also validated by Real-time PCR using STAD tissue samples. Then, based on an analysis of patient tumor RNA seq data available from the Cancer Genome Atlas (TCGA), we assessed the prognostic value of mRNA expression of the COL4A2 gene in STAD patients using K–M plotter. Results The study presented compelling evidence supporting an association between the rs34802628 polymorphism in the COL4A2 gene and susceptibility to STAD. Logistic regression analysis revealed that both the heterozygote and homozygote 4-bp del/del genotypes were significantly associated with a decreased risk of STAD, even after controlling for other variables (adjusted odds ratio [OR] = 0.663, 95% confidence interval [CI] 0.519–0.848, p = 0.037; OR = 0.422, 95% CI 0.290–0.614, p = 0.000005, respectively). Importantly, individuals carrying the 4-bp deletion allele demonstrated a notably lower risk of developing the disease (OR = 0.696, 95% CI 0.591–0.820, p = 0.000014). Furthermore, Genotype-phenotype correlation studies in human STAD tissue samples demonstrated that the higher mRNA expression levels of COL4A2 were associated with the ins allele of rs34802628. Bioinformatics analysis revealed that higher expression of the COL4A2 gene was significant with development and poor prognosis of STAD. Conclusion The results of our study provide strong evidence indicating a potential involvement of genetic variants in the COL4A2 gene in the development of STAD. Nonetheless, to validate and consolidate these findings, additional investigations incorporating larger sample sizes and functional experiments are necessary.

Autism spectrum disorder: difficulties in diagnosis and microRNA biomarkers.

We performed a PubMed search for microRNAs in autism spectrum disorder that could serve as diagnostic biomarkers in patients and selected 17 articles published from January 2008 to December 2023, of which 4 studies were performed with whole blood, 4 with blood plasma, 5 with blood serum, 1 with serum neural cell adhesion molecule L1-captured extracellular vesicles, 1 with blood cells, and 2 with peripheral blood mononuclear cells. Most of the studies involved children and the study cohorts were largely males. Many of the studies had performed microRNA sequencing or quantitative polymerase chain reaction assays to measure microRNA expression. Only five studies had used real-time polymerase chain reaction assay to validate microRNA expression in autism spectrum disorder subjects compared to controls. The microRNAs that were validated in these studies may be considered as potential candidate biomarkers for autism spectrum disorder and include miR-500a-5p, -197-5p, -424-5p, -664a-3p, -365a-3p, -619-5p, -664a- 3p, -3135a, -328-3p, and -500a-5p in blood plasma and miR-151a-3p, -181b-5p, -320a, -328, -433, -489, -572, -663a, -101-3p, -106b-5p, -19b-3p, -195-5p, and -130a-3p in blood serum of children, and miR-15b-5p and -6126 in whole blood of adults. Several important limitations were identified in the studies reviewed, and need to be taken into account in future studies. Further studies are warranted with children and adults having different levels of autism spectrum disorder severity and consideration should be given to using animal models of autism spectrum disorder to investigate the effects of suppressing or overexpressing specific microRNAs as a novel therapy.

Cathepsin C Promotes Tumorigenesis in Bladder Cancer by Activating the Wnt/β-catenin Signalling Pathway

Background: Cathepsin C (CTSC) participates in the development of numerous cancers; however, its function in bladder cancer (BCa) remains largely unknown. Methods: Bioinformatics prediction, quantitative reverse transcription polymerase chain reaction (RT-qPCR) assay, and Western blot assay were used to determine CTSC expression in BCa tissues, paracancer tissues, BCa cells, and normal uroepithelial cells (SV-HUC-1). Colony formation, cell counting kit-8 (CCK-8), and Transwell assays were utilised to ascertain the involvement of CTSC in BCa. The effect of CTSC on BCa was further studied in vivo via animal experiments. Results: CTSC exhibited a heightened expression in BCa cells and tissues; meanwhile, bladder urothelial carcinoma (BLCA) patients with enhanced CTSC expression had a remarkably reduced overall survival than those with low CTSC expression. The overexpression of CTSC substantially enhanced the activity, proliferation, migration, and invasion of BCa cells, whereas its suppression repressed the above biological phenotypes. CTSC could activate the Wnt/β-catenin signalling pathway and upregulate diaphanous-related formin 3 (DIAPH3). CTSC overexpression combined with DIAPH3 knockdown partially reversed the impact of CTSC overexpression on the biological behaviour of BCa cells and the activation of the Wnt/β-catenin signalling pathway. Conclusions: CTSC was upregulated in tissues and BCa cells, and high CTSC expression was associated with poor overall survival. CTSC could enhance the activity, proliferation, migration, and invasion of BCa cells via upregulating DIAPH3 and activating the Wnt/β-catenin pathway.

Performance of Fujifilm Dengue NS1 Antigen Rapid Diagnosis Kit Compared to Quantitative Real-Time Polymerase Chain Reaction.

Dengue is a viral infection caused by the dengue virus (DENV), transmitted to humans through the bite of infected Aedes mosquitoes. About half of the world's population is now at risk of dengue, which represents a global public health concern, especially in tropical and subtropical countries. Early detection of the viral infection is crucial to manage the disease; hence, effective rapid diagnostic tests are essential. In this study, we evaluated the performance between the new Fujifilm Dengue non-structural antigen diagnosis kit (FF NS1 kit) and the SD Bioline NS1 antigen test kit (SD NS1 kit) against the quantitative real-time polymerase chain reaction (qRT-PCR) assays. The 140 acute serum samples collected from the Yangon General Hospital and Yangon Children's Hospital, Myanmar, from 2017 to 2019 were characterised by the three assays. With the qRT-PCR as the standard, the FF NS1 kit and the SD NS1 kit exhibited sensitivity of 94.3% and 88.6%, respectively, and specificity of 100% in both kits. Moreover, the positivity rates of the FF NS1 kit and the SD NS1 kit were 97.5% and 95% in primary infection and 90% and 80% in secondary infection, respectively. Our overall results suggest that the FF NS1 kit is reliable and accurate for detecting DENV infection.

Clinical performance of the ImmuneMed Dengue NS1 Ag Rapid I test for the diagnosis of dengue fever: a diagnostic accuracy study

Background: Dengue virus (DENV) is transmitted by mosquitoes and is becoming a global threat owing to an increase in the number of cases and mortality, especially in low- and middle-income tropical countries. Rapid and easy-to-use diagnostic tests are required to differentiate dengue fever from other febrile illnesses. Methods: We evaluated the clinical performance of the ImmuneMed Dengue NS1 Ag Rapid I test (ImmuneMed, Inc.) using positive and negative sera collected from patients with confirmed DENV infection and healthy individuals, respectively. The AccuPower® ZIKV (DENV, CHIKV) multiplex real-time reverse transcription polymerase chain reaction (RT-PCR) assay (Bioneer) was used as the reference standard to confirm DENV infection. Results: One hundred DENV-positive and 161 DENV-negative samples were evaluated. Overall, the sensitivity and specificity were 100% (95% confidence interval [CI], 96%–100%) and 100% (95% CI, 98%–100%), respectively. The sensitivity and specificity were 100% for both DENV-1 and DENV- 2. The sensitivity was the same (100%) for sera collected < 3 days and ≥ 3 days from symptom onset. The performance of the ImmuneMed Dengue NS1 Ag Rapid I and realtime RT-PCR tests showed strong overall agreement. Conclusion: The ImmuneMed Dengue NS1 Ag Rapid I test was highly specific for DENV and as sensitive as RT-PCR. These findings suggest that the ImmuneMed Dengue NS1 Ag Rapid I test may be a useful point-of-care test for dengue fever.

Ensemble for evaluating diagnostic efficacy of non-invasive indices in predicting liver fibrosis in untreated hepatitis C virus population.

Hepatitis C virus (HCV) infection progresses through various phases, starting with inflammation and ending with hepatocellular carcinoma. There are several invasive and non-invasive methods to diagnose chronic HCV infection. The invasive methods have their benefits but are linked to morbidity and complications. Thus, it is important to analyze the potential of non-invasive methods as an alternative. Shear wave elastography (SWE) is a non-invasive imaging tool widely validated in clinical and research studies as a surrogate marker of liver fibrosis. Liver fibrosis determination by invasive liver biopsy and non-invasive SWE agree closely in clinical studies and therefore both are gold standards. To analyzed the diagnostic efficacy of non-invasive indices [serum fibronectin, aspartate aminotransferase to platelet ratio index (APRI), alanine aminotransferase ratio (AAR), and fibrosis-4 (FIB-4)] in relation to SWE. We have used an Artificial Intelligence method to predict the severity of liver fibrosis and uncover the complex relationship between non-invasive indices and fibrosis severity. We have conducted a hospital-based study considering 100 untreated patients detected as HCV positive using a quantitative Real-Time Polymerase Chain Reaction assay. We performed statistical and probabilistic analyses to determine the relationship between non-invasive indices and the severity of fibrosis. We also used standard diagnostic methods to measure the diagnostic accuracy for all the subjects. The results of our study showed that fibronectin is a highly accurate diagnostic tool for predicting fibrosis stages (mild, moderate, and severe). This was based on its sensitivity (100%, 92.2%, 96.2%), specificity (96%, 100%, 98.6%), Youden's index (0.960, 0.922, 0.948), area under receiver operating characteristic curve (0.999, 0.993, 0.922), and Likelihood test (LR+ > 10 and LR- < 0.1). Additionally, our Bayesian Network analysis revealed that fibronectin (> 200), AAR (> 1), APRI (> 3), and FIB-4 (> 4) were all strongly associated with patients who had severe fibrosis, with a 100% probability. We have found a strong correlation between fibronectin and liver fibrosis progression in HCV patients. Additionally, we observed that the severity of liver fibrosis increases with an increase in the non-invasive indices that we investigated.

Evaluation of a modified quantitative polymerase chain reaction assay for genus Schistosoma detection using stool and urine samples from schistosomiasis endemic areas in Kenya

Evaluation of a modified quantitative polymerase chain reaction assay for genus Schistosoma detection using stool and urine samples from schistosomiasis endemic areas in Kenya

&lt;i&gt;CDKN2B-AS1&lt;/i&gt; polymorphism rs1333049 is associated with advanced carotid artery atherosclerosis in a Slovenian population

Several studies have reported an association between the 9p21 region in the human genome and atherosclerosis. The rs1333049 polymorphism is a single nucleotide polymorphism (SNP) in CDKN2B-AS1, located in the 9p21 region. The aim of our study was to investigate the association between the rs1333049 polymorphism and advanced carotid atherosclerosis, as well as its effect on CDKN2B expression in endarterectomy sequesters. In our case-control study, we included 881 participants, divided into two groups. The case group comprised 308 participants with advanced atherosclerosis of the internal or common carotid artery (stenosis &gt; 75 %) who underwent a revascularization procedure. The control group included 573 participants without hemodynamically significant carotid atherosclerosis. We analyzed the rs1333049 polymorphism using the StepOne real-time polymerase chain reaction (PCR) and TaqMan SNP genotyping assay. We found a statistically significant association according to the co-dominant (P=0.014, OR=3.29, 95% CI: 1.32-8.91, and P=0.015, OR=2.50, 95% CI: 1.22-5.37) and dominant (P=0.006, OR=2.74, 95% CI: 1.36-5.71) models. We performed immunohistochemical analysis of CDKN2B expression on 26 endarterectomy sequesters. The C allele of rs1333049 was associated with a lower numerical area density of CDKN2B-positive cells in atherosclerotic plaques. In conclusion, the C allele of the rs1333049 SNP is associated with an increased risk of developing advanced carotid atherosclerosis and lower CDKN2B expression in the plaques.