scholarly journals Evaluation validation of a qPCR curve analysis method and conventional approaches

BMC Genomics ◽  
2021 ◽  
Vol 22 (S5) ◽  
Author(s):  
Yashu Zhang ◽  
Hongping Li ◽  
Shucheng Shang ◽  
Shuoyu Meng ◽  
Ting Lin ◽  
...  
Keyword(s):  
Quantitative Polymerase Chain Reaction ◽  
Statistical Significance ◽  
Fold Increase ◽  
Curve Analysis ◽  
Evaluation Index System ◽  
Analysis Method ◽  
Concentration Gradients ◽  
Algorithm Performance ◽  
Partial Data ◽  
Clinical Biomarker

Abstract Background Reverse Transcription quantitative polymerase chain reaction (RT-qPCR) is a sensitive and reliable method for mRNA quantification and rapid analysis of gene expression from a large number of starting templates. It is based on the statistical significance of the beginning of exponential phase in real-time PCR kinetics, reflecting quantitative cycle of the initial target quantity and the efficiency of the PCR reaction (the fold increase of product per cycle). Results We used the large clinical biomarker dataset and 94-replicates-4-dilutions set which was published previously as research tools, then proposed a new qPCR curve analysis method——CqMAN, to determine the position of quantitative cycle as well as the efficiency of the PCR reaction and applied in the calculations. To verify algorithm performance, 20 genes from biomarker and partial data with concentration gradients from 94-replicates-4-dilutions set of MYCN gene were used to compare our method with various publicly available methods and established a suitable evaluation index system. Conclusions The results show that CqMAN method is comparable to other methods and can be a feasible method which applied to our self-developed qPCR data processing and analysis software, providing a simple tool for qPCR analysis.

scholarly journals Evaluation validation of a qPCR curve analysis method and conventional approaches

2020 ◽  
Author(s):  
Yashu Zhang ◽  
Hongping Li ◽  
Shucheng Shang ◽  
Shuoyu Meng ◽  
Ting Lin ◽  
...  
Keyword(s):  
Real Time ◽  
Quantitative Polymerase Chain Reaction ◽  
Statistical Significance ◽  
Fold Increase ◽  
Curve Analysis ◽  
Evaluation Index System ◽  
Analysis Method ◽  
Concentration Gradients ◽  
Algorithm Performance ◽  
Partial Data

AbstractReal-time quantitative polymerase chain reaction (qPCR) is a sensitive and reliable method for mRNA quantification and rapid analysis of gene expression from a large number of starting templates. It is based on the statistical significance of the beginning of exponential phase in real-time PCR kinetics, reflecting quantitative cycle of the initial target quantity and the efficiency of the PCR reaction (the fold increase of product per cycle). We used the large clinical biomaker dataset and 94-replicates-4-dilutions set which was published previously as research tools, then proposed a new qPCR curve analysis method——CqMAN, to determine the position of quantitative cycle as well as the efficiency of the PCR reaction and applied in the calculations. To verify algorithm performance, 20 genes from biomarker and partial data with concentration gradients from 94-replicates-4-dilutions set of MYCN gene were used to compare various publicly available curve analysis methods with our method and established a suitable evaluation index system. The results show that CqMAN method is comparable to other methods and can be a feasible method which applied to our self-developed qPCR data processing and analysis software, providing a simple tool for qPCR analysis.

Determination of the latent heat of fusion and solid fraction evolution of metals and alloys by an improved cooling curve analysis method

2019 ◽  
Vol 140 (4) ◽  
pp. 1825-1836 ◽  
Author(s):  
Carlos González-Rivera ◽  
Anthony Harrup ◽  
Carla Aguilar ◽  
Adrián M. Amaro-Villeda ◽  
Marco A. Ramírez-Argáez
Keyword(s):  
Latent Heat ◽  
Solid Fraction ◽  
Metals And Alloys ◽  
Curve Analysis ◽  
Cooling Curve ◽  
Heat Of Fusion ◽  
Analysis Method ◽  
Latent Heat Of Fusion ◽  
Cooling Curve Analysis

scholarly journals C/EBPα directs monocytic commitment of primary myeloid progenitors

Blood ◽  
2006 ◽  
Vol 108 (4) ◽  
pp. 1223-1229 ◽  
Author(s):  
Dehua Wang ◽  
Jenice D'Costa ◽  
Curt I. Civin ◽  
Alan D. Friedman
Keyword(s):  
Quantitative Polymerase Chain Reaction ◽  
Fold Increase ◽  
Pcr Assay ◽  
Gm Csf ◽  
Specific Effects ◽  
Proliferation And Apoptosis ◽  
Polymerase Chain ◽  
Lineage Markers ◽  
Transcriptional Induction

Abstract C/EBPα is required for generation of granulocyte-monocyte progenitors, but the subsequent role of C/EBPα in myeloid lineage commitment remains uncertain. We transduced murine marrow cells with C/EBPα-estradiol receptor (ER) or empty vector and subjected these to lineage depletion just prior to culture in estradiol with myeloid cytokines. This protocol limits biases due to lineage-specific effects on developmental kinetics, proliferation, and apoptosis. Also, lowering the dose of estradiol reduced activated C/EBPα-ER to near the physiologic range. C/EBPα-ER increased Mac1+/Gr1–/MPO–/low monocytes 1.9-fold while reducing Mac1+/Gr1+/MPOhi granulocytes 2.5-fold at 48 hours, even in 0.01 μM estradiol. This pattern was confirmed morphologically and by quantitative polymerase chain reaction (PCR) assay of lineage markers. To directly assess effects on immature progenitors, transduced cells were cultured for 1 day with and then in methylcellulose without estradiol. A 2-fold increase in monocytic compared with granulocytic colonies was observed in IL-3/IL-6/SCF or GM-CSF, but not G-CSF, even in 0.01 μM estradiol. C/EBPα-ER induced PU.1 mRNA, and PU.1-ER stimulated monocytic development, suggesting that transcriptional induction of PU.1 by C/EBPα contributes to monopoiesis. A C/EBPα variant incapable of zippering with c-Jun did not induce monopoiesis, and a variant unable to bind NF-κB p50 stimulated granulopoiesis, suggesting their cooperation with C/EBPα during monocytic commitment.

scholarly journals Ticagrelor and clopidogrel suppress NF-κB to treat acute coronary syndrome

2019 ◽  
Author(s):  
Zhuyin Jia ◽  
Yiwei Huang ◽  
Xiaojun Ji ◽  
Jiaju Sun ◽  
Guosheng Fu
Keyword(s):  
Cell Cycle ◽  
Acute Coronary Syndrome ◽  
Cell Migration ◽  
Cell Viability ◽  
Umbilical Vein ◽  
Quantitative Polymerase Chain Reaction ◽  
Statistical Significance ◽  
Inflammatory Factors ◽  
Mrna Levels ◽  
Coronary Syndrome

Abstract Background: Inflammatory cytokines are involved in acute coronary syndrome (ACS),and NF-kB is the central regulator of inflammation. Moreover, ticagrelor and clopidogrelcan prevent thrombotic events and improve the care of patients with ACS. Thus, we speculated that ticagrelor and clopidogrel relieve ACS by regulating NF-kB pathway. Methods: After human umbilical vein endothelial cells (HUVECs) were cultured with ticagrelor or clopidogrel and given lipopolysaccharide (LPS) and CD14, the mRNA levels of related inflammatory factors, the protein level changes of molecules in the NF-kB pathway, and the changes in cell viability, apoptosis and the cell cycle, cell migration, vascular formation and other vital activities were detected using quantitative Polymerase chain reaction (qPCR), Western blotting and immunofluorescence assay, CCK8， flow cytometry, transwell assay, matrigel, respectively. All data was expressed as the mean ± S.D. The statistical significance of data was assessedby an unpaired two-tailed t-test. Results: Ticagrelor and clopidogrel can suppress the NF-kB pathway by inhibiting the phosphorylation and entry into the nucleus of p65, restraining the degradation of IKBa, improving cell viability, restoring the cell cycle, cell migration and angiogenic ability, and inhibiting apoptosis. Conclusions: Ticagrelor and clopidogrel alleviate cellular dysfunction through suppressing NF-kB signaling to treat acute coronary syndrome.

A novel duplex SYBR Green real-time PCR with melting curve analysis method for beef adulteration detection

2021 ◽  
Vol 338 ◽  
pp. 127932
Author(s):  
Jiapeng Li ◽  
Yixuan Wei ◽  
Jinchun Li ◽  
Ruixi Liu ◽  
Suigen Xu ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Melting Curve ◽  
Curve Analysis ◽  
Sybr Green ◽  
Melting Curve Analysis ◽  
Analysis Method

scholarly journals Dynamic Comprehensive Benefit Evaluation of the Transnational Power Grid Interconnection Project Based on Combination Weighting and TOPSIS Grey Projection Method

2018 ◽  
Vol 10 (12) ◽  
pp. 4672 ◽  
Author(s):  
Jinying Li ◽  
Jiaming Xu ◽  
Xin Tan
Keyword(s):  
Projection Method ◽  
Index System ◽  
Global Economy ◽  
Least Squares Method ◽  
Power Grid ◽  
Rapid Development ◽  
Order Relation ◽  
Evaluation Index System ◽  
Analysis Method ◽  
Grid Interconnection

With the rapid development of the global economy, the interconnection of power grids has become an objective law and a trend of the power industry development. The implementation of power grid interconnection projects, especially transnational power grid interconnection projects, will bring us substantial benefits. To demonstrate these benefits comprehensively, we designed a comprehensive evaluation index system with multiple international engineering characteristics. The index system takes the influencing factors of economic, social, environmental and technical benefits into account. In order to improve the rigidity and power of weight determination, we proposed the least squares method which combines the order relation method and the factor analysis method. Furthermore, the limitation of the one-way evaluation was effectively overcome by combining TOPSIS (Technique for Order Preference by Similarity to an Ideal Solution), grey relation analysis method and vector projection method. In addition, we adjusted the potential impact of the time on evaluation by using the quadratic weighted algorithm, so that we can dynamically evaluate the comprehensive benefits. Finally, we verified the established index system and evaluation model through an example of eight different investment plans of a transnational high voltage direct current (HVDC) transmission project. Altogether, results from this paper will provide a guidance reference and decision support for the grid corporation to invest in transnational power grid interconnection projects.

scholarly journals Impact of season and geography on CompEx Asthma: a composite end-point for exacerbations

2020 ◽  
Vol 6 (4) ◽  
pp. 00246-2020
Author(s):  
Alexandra Jauhiainen ◽  
Lieke E.J.M. Scheepers ◽  
Anne L. Fuhlbrigge ◽  
Tim Harrison ◽  
James Zangrilli ◽  
...  
Keyword(s):  
Eastern Europe ◽  
Randomised Controlled Trials ◽  
Treatment Effects ◽  
Statistical Significance ◽  
Fold Increase ◽  
Controlled Trials ◽  
End Point ◽  
Geographical Regions ◽  
Randomised Controlled ◽  
Event Rates

BackgroundCompEx Asthma, a novel composite end-point combining severe exacerbations (SevEx) with asthma-worsening events, was recently developed. Further characterisation of CompEx Asthma is needed to illustrate the applicability of this end-point. The objective was to evaluate CompEx Asthma as a rate end-point to determine how seasonal and geographical factors impact this novel outcome.MethodsSeven 24–56-week randomised controlled trials of budesonide/formoterol (BUD/FORM) and benralizumab were analysed. Annualised event rates (AERs) and treatment effects (hazard ratio (HR)) were analysed with Poisson and Andersen–Gill models, respectively. Seasonality was analysed by month and five geographical regions were evaluated.ResultsThe studies included 10 815 patients (63% female, mean age 42–49 years). CompEx Asthma AER mirrored seasonal variations in SevEx AER. CompEx Asthma AERs were higher versus SevEx in BUD/FORM and benralizumab trials (range 2.7–4.5-fold and 1.3–2.0-fold increase, respectively) and were less variable versus SevEx between regions (ratios of greatest:smallest AERs: 1.36 for CompEx versus 2.28 for SevEx (BUD/FORM); 1.81 for CompEx versus 2.22 for SevEx (benralizumab)). Treatment effects for CompEx Asthma and SevEx were generally similar across regions and months. However, in Eastern Europe, where SevEx rates were lowest, treatment effect was greater with CompEx Asthma versus SevEx, reaching statistical significance in the benralizumab studies (HR (95% CI): 0.67 (0.53–0.85) versus 0.87 (0.65–1.15)).ConclusionThis study confirmed the reliability of CompEx Asthma as a rate end-point and allowed detection of variations in seasonal SevEx rates, reduction of variation in rates across regions and potential greater sensitivity to treatment effects.

The Comprehensive Evaluation on Energy Conservation and Emission Reduction about the Efficiency on Industry of Jiangsu Province

2012 ◽  
Vol 610-613 ◽  
pp. 965-969
Author(s):  
Geng Wang ◽  
Fang Fei Gao
Keyword(s):  
Energy Conservation ◽  
Emission Reduction ◽  
Comprehensive Evaluation ◽  
Principal Component ◽  
Jiangsu Province ◽  
Evaluation Index System ◽  
Analysis Method ◽  
Evaluation Of Performance ◽  
Classification Evaluation ◽  
The Empirical Analysis

From the perspective of city, Jiangsu province enterprise energy conservation and emission reduction in the evaluation of performance is studied. First, the energy conservation and emission reduction of performance comprehensive evaluation index system is established. Second, using the principal component analysis method to 13 major cities have the empirical analysis and comparative study. Finally, a comprehensive and three classification evaluation list is given.

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