scholarly journals Potential mechanism of circRNA_000585 in cholangiocarcinoma

2021 ◽  
Vol 49 (6) ◽  
pp. 030006052110245
Author(s):  
Fengming Yi ◽  
Longxiang Xin ◽  
Long Feng
Keyword(s):  
Bioinformatics Analysis ◽  
Circular Rna ◽  
Vital Role ◽  
Cancer Tissue ◽  
Microarray Hybridization ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Qrt Pcr ◽  
Polymerase Chain ◽  
Cancer Tissues

Objective Circular RNA (circRNA) plays a vital role in the development and progression of malignancies, however, the function of circRNAs in cholangiocarcinoma (CCA) remains unexplored. The aim of this study was to investigate circRNA expression in CCA versus para-cancer tissues, and elucidate any potential associated mechanisms. Methods Differential expression of circRNAs between CCA and para-cancer tissue was analysed by microarray hybridization, and validated by real-time quantitative reverse transcription–polymerase chain reaction (qRT–PCR). The downstream pathway was investigated using bioinformatics and qRT–PCR. Results Microarray hybridization revealed 10 circRNAs with > 3-fold increased expression versus para-cancer (circRNA_002172, circRNA_002144, circRNA_001588, circRNA_000166, circRNA_000585, circRNA_000167, circRNA_402608, circRNA_006853, circRNA_001589, circRNA_008882), and three circRNAs with > 3-fold decreased expression (circRNA_406083, circRNA_104940, circRNA_006349). CircRNA_000585 was shown by qRT-PCR to be upregulated in tumour versus paired para-cancer tissue from 15 patients with CCA. Bioinformatics analysis revealed a potential pathway comprising circRNA_000585/microRNA-615-5p/angiomotin (AMOT)/Yes associated protein 1 (YAP) in CCA. RT–PCR validation of crucial molecule expression showed downregulation of miR-615-5p, and upregulation of AMOT and YAP in CCA tumours. Conclusion Multiple circRNAs are dysregulated in CCA. CircRNA_000585 is upregulated in CCA, and may function by a circRNA_000585/miR-615-5p/AMOT/YAP pathway, which may be a novel CCA pathway.

scholarly journals MiRNA-107 enhances the malignant progression of pancreatic cancer by targeting TGFBR3

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0249375
Author(s):  
Tingke Tian ◽  
Quanzhong Yang ◽  
Cuijuan Zhang ◽  
Xiaokun Li ◽  
Jiancheng Cheng
Keyword(s):  
Pancreatic Cancer ◽  
Molecular Mechanisms ◽  
Bioinformatics Analysis ◽  
Therapeutic Targets ◽  
Biological Functions ◽  
Chain Reaction ◽  
Invasion And Migration ◽  
Qrt Pcr ◽  
Polymerase Chain ◽  
And Migration

Background The prognosis of pancreatic cancer (PC) is relatively dismal due to the lack of effective therapy. In this study, we explored the specific functions and molecular mechanisms of miR-107 to uncover effective therapeutic targets for PC. Method The miR-107 expression in PC cell lines was assessed via quantitative real-time polymerase chain reaction (qRT-PCR). Besides, online bioinformatics analysis was adopted to predict the underlying targets of miR-107. Meanwhile, TCGA database was employed to explore the prognosis of PC patients. In addition, MTT and transwell assays were conducted to explore the PC cells’ biological functions. Result MiR-107 was remarkably increased in PC cells which could promote the proliferation, invasion and migration of PC cells. In addition, miR-107 could directly down-regulate TGFBR3 expression through binding to TGFBR3 3’UTR. Survival analysis from TCGA suggested that PC patients with higher miR-107 expression was significantly involved in poorer prognosis. Conclusion We concluded that miR-107 promoted proliferation, invasion and migration of PC cells via targeting TGFBR3, which may provide novel underlying therapeutic targets.

scholarly journals Comprehensive Study of Coronavirus Disease 2019 (COVID-19) Classification based on Deep Convolution Neural Networks

2021 ◽  
Vol 102 ◽  
pp. 04007
Author(s):  
Miyuka Nakamura ◽  
Jiangkun Wang ◽  
Sinchhean Phea ◽  
Abderazek Ben Abdallah
Keyword(s):  
Vital Role ◽  
Software Implementation ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Test Dataset ◽  
The World ◽  
Biomedical Diagnosis ◽  
Polymerase Chain ◽  
Network Software ◽  
Comprehensive Study

Artificial Intelligence (AI) has recently become a topic of study in different applications, including healthcare, in which timely detection of anomalies can play a vital role in patients health monitoring. The coronavirus disease 2019 (COVID-19), caused by the SARS-CoV-2 virus, colloquially known as the Coronavirus, disrupts large parts of the world. The standard way to test for COVID-19 is Reverse Transcription Polymerase Chain Reaction (RT-PCR), which uses collected samples from the patient. This paper presents an efficient convolution neural network software implementation for COVID-19 and other pneumonia disease detection targeted for an AI-enabled smart biomedical diagnosis system (AIRBiS). From the evaluation results, we found that the classification accuracy of the abnormal (COVID-19 and pneumonia) test dataset is over 97.18%. On the other hand, the accuracy of the normal is no more than 71.37%. We discussed the possible problems and proposals for further optimization.

scholarly journals The genotyping of Infectious bronchitis virus in Taiwan by a multiplex amplification refractory mutation system reverse transcription polymerase chain reaction

2014 ◽  
Vol 26 (6) ◽  
pp. 721-733 ◽  
Author(s):  
Shr-Wei Huang ◽  
Chia-Fang Ho ◽  
Kun-Wei Chan ◽  
Min-Chung Cheng ◽  
Jui-Hung Shien ◽  
...  
Keyword(s):  
Amplification Refractory Mutation System ◽  
Wild Type ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Infectious Bronchitis ◽  
Melting Temperatures ◽  
Qrt Pcr ◽  
Multiplex Amplification ◽  
Mutation System ◽  
Polymerase Chain

Infectious bronchitis virus (IBV; Avian coronavirus) causes acute respiratory and reproductive and urogenital diseases in chickens. Following sequence alignment of IBV strains, a combination of selective primer sets was designed to individually amplify the IBV wild-type and vaccine strains using a multiplex amplification refractory mutation system reverse transcription polymerase chain reaction (ARMS RT-PCR) approach. This system was shown to discriminate the IBV wild-type and vaccine strains. Moreover, an ARMS real-time RT-PCR (ARMS qRT-PCR) was combined with a high-resolution analysis (HRMA) to establish a melt curve analysis program. The specificity of the ARMS RT-PCR and the ARMS qRT-PCR was verified using unrelated avian viruses. Different melting temperatures and distinct normalized and shifted melting curve patterns for the IBV Mass, IBV H120, IBV TW-I, and IBV TW-II strains were detected. The new assays were used on samples of lung and trachea as well as virus from allantoic fluid and cell culture. In addition to being able to detect the presence of IBV vaccine and wild-type strains by ARMS RT-PCR, the IBV Mass, IBV H120, IBV TW-I, and IBV TW-II strains were distinguished using ARMS qRT-PCR by their melting temperatures and by HRMA. These approaches have acceptable sensitivities and specificities and therefore should be able to serve as options when carrying out differential diagnosis of IBV in Taiwan and China.

scholarly journals Hsa_circ_0001461 as a novel biomarker in patients with primary focal segmental glomerulosclerosis

2021 ◽  
Author(s):  
Xiaoyi Cai ◽  
Jiayi Zhang ◽  
Mei Tan ◽  
Zichuan Xu ◽  
Huiying Deng ◽  
...  
Keyword(s):  
Focal Segmental Glomerulosclerosis ◽  
Minimal Change Disease ◽  
Operating Characteristic ◽  
Bioinformatics Analysis ◽  
Circular Rnas ◽  
Chain Reaction ◽  
Qrt Pcr ◽  
Segmental Glomerulosclerosis ◽  
Non Coding Rnas ◽  
Polymerase Chain

IntroductionCircular RNAs (circRNAs), a novel class of non-coding RNAs, have been implicated in various diseases and are considered to play an important role in physiological and pathological processes. We aimed to profile renal circRNA in children with primary focal segmental glomerulosclerosis (FSGS) and predict the potential mechanism underlying the pathogenesis of FSGS.Material and methodsA global circRNA expression analysis was performed in renal tissues from patients with FSGS (n=3) and controls (n=3). Quantitative real-time polymerase chain reaction (qRT-PCR) was conducted to validate the expression levels of three circRNAs in a cohort of 44 patients with FSGS, 44 age-matched healthy controls, and 15 patients with minimal change disease (MCD).ResultsA total of 152 circRNAs were differentially expressed in patients with FSGS compared with controls. Hsa_circ_0001461 and hsa_circ_0000605 were significantly increased in patients with FSGS compared with controls, as determined by qRT-PCR (p < 0.001). The receiver operating characteristic (ROC) curve areas of hsa_circ_0001461 and hsa_circ_0000605 were 0.948 and 0.934, respectively. Hsa_circ_0001461 was significantly elevated in patients with FSGS compared with those with MCD and was correlated with 24 h urinary protein in patients with FSGS (r = 0.732, p < 0.001). Bioinformatics analysis predicted mir-30a interaction with hsa_circ_0001461. Mir-30a was negatively correlated with the renal hsa_circ_0001461 level (r = -0.90, p < 0.001).ConclusionsHsa_circ_0001461 is identified as a novel biomarker in children with FSGS and might provide insights into the mechanism of FSGS pathogenesis.

1504: Molecular Diagnosis and Staging of Prostate Cancer Using Clusterin in Real Time Reverse Transcription Polymerase Chain Reaction (RT-PCR)

2006 ◽  
Vol 175 (4S) ◽  
pp. 485-486
Author(s):  
Sabarinath B. Nair ◽  
Christodoulos Pipinikas ◽  
Roger Kirby ◽  
Nick Carter ◽  
Christiane Fenske
Keyword(s):  
Prostate Cancer ◽  
Polymerase Chain Reaction ◽  
Real Time ◽  
Molecular Diagnosis ◽  
Reverse Transcription ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Polymerase Chain

Expression of Platelet Membrane Glycoprotein V in Human Megakaryocytes and Megakaryocytic Cell Lines: A Study Using a Novel Monoclonal Antibody against GPV

1994 ◽  
Vol 72 (05) ◽  
pp. 762-769 ◽  
Author(s):  
Toshiro Takafuta ◽  
Kingo Fujirmura ◽  
Hironori Kawano ◽  
Masaaki Noda ◽  
Tetsuro Fujimoto ◽  
...  
Keyword(s):  
Monoclonal Antibody ◽  
Cell Lines ◽  
Immunohistochemical Analysis ◽  
Specific Protein ◽  
Platelet Membrane ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Flow Cytometric ◽  
Polymerase Chain ◽  
Megakaryocytic Cell

SummaryGlycoprotein V (GPV) is a platelet membrane protein with a molecular weight of 82 kD, and one of the leucine rich glycoproteins (LRG). By reverse transcription-polymerase chain reaction (RT-PCR), GPV cDNA was amplified from mRNA of platelets and megakaryocytic cell lines. However, since there are few reports indicating whether GPV protein is expressed in megakaryocytes as a lineage and maturation specific protein, we studied the GPV expression at the protein level by using a novel monoclonal antibody (1D9) recognizing GPV. Flow cytometric and immunohistochemical analysis indicated that GPV was detected on the surface and in the cytoplasm of only the megakaryocytes in bone marrow aspirates. In a megakaryocytic cell line UT-7, GPV antigen increased after treatment with phorbol-12-myri-state-13-acetate (PMA). These data indicate that only megakaryocytes specifically express the GPV protein among hematopoietic cells and that the expression of GPV increases with differentiation of the megakaryocyte as GPIb-IX complex.

Polymerase chain reaction amplification and typing of rotavirus in environmental samples

1995 ◽  
Vol 31 (5-6) ◽  
pp. 371-374 ◽  
Author(s):  
R. Gajardo ◽  
R. M. Pintó ◽  
A. Bosch
Keyword(s):  
Polymerase Chain Reaction ◽  
Environmental Samples ◽  
Polymerase Chain Reaction Amplification ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Pcr Assay ◽  
Group A ◽  
Reaction Amplification ◽  
Stool Specimens ◽  
Polymerase Chain

A reverse transcription polymerase chain reaction (RT-PCR) assay is described that has been developed for the detection and serotyping of group A rotavirus in stool specimens and concentrated and non-concentrated sewage specimens.

scholarly journals Machine Learning Prediction of SARS-CoV-2 Polymerase Chain Reaction Results with Routine Blood Tests

2020 ◽  
Author(s):  
Thomas Tschoellitsch ◽  
Martin Dünser ◽  
Carl Böck ◽  
Karin Schwarzbauer ◽  
Jens Meier
Keyword(s):  
Machine Learning ◽  
Polymerase Chain Reaction ◽  
Characteristic Curve ◽  
Cohort Analysis ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Blood Tests ◽  
Routine Blood ◽  
Machine Learning Model ◽  
Polymerase Chain

Abstract Objective The diagnosis of COVID-19 is based on the detection of SARS-CoV-2 in respiratory secretions, blood, or stool. Currently, reverse transcription polymerase chain reaction (RT-PCR) is the most commonly used method to test for SARS-CoV-2. Methods In this retrospective cohort analysis, we evaluated whether machine learning could exclude SARS-CoV-2 infection using routinely available laboratory values. A Random Forests algorithm with 1353 unique features was trained to predict the RT-PCR results. Results Out of 12,848 patients undergoing SARS-CoV-2 testing, routine blood tests were simultaneously performed in 1528 patients. The machine learning model could predict SARS-CoV-2 test results with an accuracy of 86% and an area under the receiver operating characteristic curve of 0.90. Conclusion Machine learning methods can reliably predict a negative SARS-CoV-2 RT-PCR test result using standard blood tests.

scholarly journals Report of a Confirmed SARS-CoV-2 Positive Newborn after Delivery Despite Negative SARS-CoV-2 Testing on Both Parents

2021 ◽  
Vol 11 (02) ◽  
pp. e80-e83
Author(s):  
Benjamin R. Harding ◽  
Farha Vora
Keyword(s):  
Neonatal Intensive Care ◽  
Community Hospital ◽  
Material Testing ◽  
Term Infant ◽  
Accurate Diagnosis ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Potential Case ◽  
Polymerase Chain ◽  
Negative Material

AbstractWe present a case of a term infant born to an asymptomatic mother at a community hospital who required transfer to a local neonatal intensive care unit (NICU) immediately after birth for respiratory distress. The infant was tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at 24 hours of life by reverse transcription polymerase chain reaction (RT-PCR) testing due to the absence of prenatal maternal COVID-19 testing and was found to be positive for SARS-CoV-2 at that time. A second RT-PCR test was obtained on the infant on day of life (DOL) 4 and was also positive, confirming an accurate diagnosis of COVID-19 disease in the infant. Both the mother and father remained asymptomatic and concomitantly tested negative for SARS-CoV-2 on two separate occasions. The infant subsequently clinically improved and was discharged without any complications. This case raises the potential concern for two unreported newborn issues related to COVID-19. First, the potential unreliability of negative maternal COVID-19 testing surrounding the time of delivery as it relates to routine newborn testing and isolation needs, and second, if the negative material testing was accurate, this raises the concern for a potential case of nosocomial COVID-19 infection within the first 24 hours of life.

Sign in / Sign up

Export Citation Format

Share Document