Savitzky–Golay smoothing and differentiation for polymerase chain reaction quantification

2018 ◽  
Vol 96 (3) ◽  
pp. 380-389 ◽  
Author(s):  
Charles Gaudreault ◽  
Joanny Salvas ◽  
Joël Sirois
Keyword(s):  
Relative Error ◽  
Logistic Model ◽  
Data Sets ◽  
Threshold Method ◽  
Chain Reaction ◽  
Quantification Method ◽  
Curve Modeling ◽  
Polymerase Chain ◽  
The Impact ◽  
Inter Assay Variation

In quantitative PCR (qPCR), replicates can minimize the impact of intra-assay variation; however, inter-assay variations must be minimized to obtain a robust quantification method. The method proposed in this study uses Savitzky–Golay smoothing and differentiation (SGSD) to identify a derivative-maximum-based cycle of quantification. It does not rely on curve modeling, as is the case with many existing techniques. PCR fluorescence data sets challenged for inter-assay variations (different thermocycler units, different reagents batches, different operators, different standard curves, and different labs) were used for the evaluation. The algorithm was compared with a four-parameter logistic model (4PLM) method, the Cy0 method, and the threshold method. The SGSD method compared favourably with all methods in terms of inter-assay variation. SGSD was statistically different from the 4PLM (P = 0.03), Cy0 (P = 0.05), and threshold (P = 0.004) methods on relative error comparison basis. For intra-assay variations, SGSD outperformed the threshold method (P = 0.005) and equalled the 4PLM and Cy0 methods (P > 0.05) on relative error basis. Our results demonstrate that the SGSD method could potentially be an alternative to sigmoid modeling based methods (4PLM and Cy0) when PCR data are challenged for inter-assay variations.

scholarly journals Clinical outcomes of concomitant use of enteral and intravenous sedatives and analgesics in mechanically ventilated patients with COVID-19

2021 ◽  
Author(s):  
Nayoung Kang ◽  
Mohammed A Alrashed ◽  
Eric M Place ◽  
Phuongthao T Nguyen ◽  
Stephen J Perona ◽  
...  
Keyword(s):  
Mechanical Ventilation ◽  
Invasive Mechanical Ventilation ◽  
Institutional Review Board ◽  
Chain Reaction ◽  
Mechanically Ventilated ◽  
Ventilation Time ◽  
Institutional Review ◽  
Significant Difference ◽  
Polymerase Chain ◽  
The Impact

Abstract Disclaimer In an effort to expedite the publication of articles related to the COVID-19 pandemic, AJHP is posting these manuscripts online as soon as possible after acceptance. Accepted manuscripts have been peer-reviewed and copyedited, but are posted online before technical formatting and author proofing. These manuscripts are not the final version of record and will be replaced with the final article (formatted per AJHP style and proofed by the authors) at a later time. Purpose To evaluate potential differences in days on mechanical ventilation for patients with coronavirus disease 2019 (COVID-19) based on route of administration of analgesic and sedative medications: intravenous (IV) alone vs IV + enteral (EN). Summary This institutional review board–approved study evaluated ventilation time and fentanyl or midazolam requirements with or without concurrent EN hydromorphone and lorazepam. Patients were included in the study if they were 18 to 89 years old and were admitted to the intensive care unit with a positive severe acute respiratory syndrome coronavirus 2 reverse transcription and polymerase chain reaction or antigen test and respiratory failure requiring invasive mechanical ventilation for more than 72 hours. In total, 100 patients were evaluated, 60 in the IV-only group and 40 in the IV + EN group. There was not a significant difference in ventilation time between the groups (mean [SD], 19.6 [12.8] days for IV + EN vs 15.6 [11.2] days for IV only; P = 0.104). However, fentanyl (2,064 [847] μg vs 2,443 [779] μg; P < 0.001) and midazolam (137 [72] mg vs 158 [70] mg; P = 0.004) requirements on day 3 were significantly higher in the IV-only group, and the increase in fentanyl requirements from day 1 to day 3 was greater in the IV-only group than in the IV + EN group (378 [625] μg vs 34 [971] μg; P = 0.033). Conclusion Addition of EN analgesic and sedative medications to those administered by the IV route did not change the duration of mechanical ventilation in patients with COVID-19, but the combination may reduce IV opioid requirements, decreasing the impact of IV medication shortages.

Detection of Aspergillus fumigatus by Polymerase Chain Reaction (PCR)

2019 ◽  
Vol 10 (04) ◽  
pp. 655-661
Author(s):  
Zainab H Abood AL-Asadi
Keyword(s):  
Polymerase Chain Reaction ◽  
Aspergillus Fumigatus ◽  
Oligonucleotide Primer ◽  
Rrna Gene ◽  
Fungal Culture ◽  
Chain Reaction ◽  
Isolation And Identification ◽  
Internal Transcribed Spacer Region ◽  
Polymerase Chain ◽  
The Impact

Aspergillosis refers to fungi infections of the respiratory tract caused by Aspergillus species, especially Aspergillus fumigatus. Infection of A. fumigatus was increased in the last few years due to either resistances to antibiotics or the influence of other factors such as other fungal infections. The present study aimed to review the impact of Aspergillus fumigatus in Aspergillosis cases, and study the role of Singleplex PCR for amplification of ITS1, ITS4 of rRNA gene in the detection of fungal isolate. In this study, One hundred sputum samples were collected from patients admitted to the specialize chest and respiratory diseases center / Baghdad who were suffering from respiratory problems. During these studied, molds were isolation and identification based on Conventional method (Direct microscopy by using 10% KOH, and fungal culture was done on Sabouraud Dextrose agar supplemented with chloramphenicol and on Czapek-Dox agar incubated at 37°C and examined for 3-7 days then macroscopic, microscopic examination of the colony by(lactophenol cotton blue stain )and molecular methods by using Polymerase chain reaction (PCR)technique for identification. The 10% KOH examination was positive for 35 cases, while laboratory culturing was positive for 53 cases. Aspergillus sp were isolated from 44(83%) patients; A. fumigatus was isolated in 23 (42. 4%) patients while A. flavus, A. niger, and A. terreus were isolated from 11 (20. 08%), (13. 2%) and 3 (5. 7%) patients respectively, also isolated Penicillium spp. at percentage 1(1. 9%). In this study. The ages of participants ranged from 10-70years with a mean age of 34years, the males were more susceptible to fungal infection, were recorded 35/53 (66. 3), compared to females were 18/53 (33. 96). The infection of fungi was more prevalent in ages 30-40recorded 26(53. 06%) followed by ages 40-50, 13(26. 5), while the lowest infection recorded in the age group 10- 20 years was 2(2. 04%). DNA isolated from twenty-three A. fumigatus isolates was used as a template, and the specific of oligonucleotide primer sequences were used in conventional PCR to detect the presence of internal transcribed spacer region ( ITS) region of the rRNA gene for Aspergillus fumigates. The results of the PCR amplification of the rRNA gene showed that this gene was present in 19 samples out 23 positive samples which isolation with a PCR product size of approximated 385 bp, while 4 samples out 23 positive samples showed negative results for the presence of this gene as indicated by the absence of the PCR products in their relevant lanes. Statistical analysis revealed that the PCR to have a sensitivity of 95. 1% in the detection of Aspergillus fumigatus in Aspergillosis cases. Polymerase chain reaction (PCR) is a rapid, specific, and sensitive method to detect Aspergillus fumigatus in aspergillosis cases of humans.

scholarly journals PRIMEval: Optimization and screening of multiplex oligonucleotide assays

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Rick Conzemius ◽  
Michaela Hendling ◽  
Stephan Pabinger ◽  
Ivan Barišić
Keyword(s):  
In Silico ◽  
Multiplex Polymerase Chain Reaction ◽  
Data Sets ◽  
Use Case ◽  
Chain Reaction ◽  
Experimental Conditions ◽  
Oligonucleotide Hybridization ◽  
Polymerase Chain ◽  
Derived Data ◽  
By Products

AbstractThe development of multiplex polymerase chain reaction and microarray assays is challenging due to primer dimer formation, unspecific hybridization events, the generation of unspecific by-products, primer depletion, and thus lower amplification efficiencies. We have developed a software workflow with three underlying algorithms that differ in their use case and specificity, allowing the complete in silico evaluation of such assays on user-derived data sets. We experimentally evaluated the method for the prediction of oligonucleotide hybridization events including resulting products and probes, self-dimers, cross-dimers and hairpins at different experimental conditions. The developed method allows explaining the observed artefacts through in silico WGS data and thermodynamic predictions. PRIMEval is available publicly at https://primeval.ait.ac.at.

scholarly journals The impact of COL1A1 and COL6A1 expression on hypospadias and penile curvature severity

BMC Urology ◽  
2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Prahara Yuri ◽  
Gunadi ◽  
Rahmadani Puji Lestari ◽  
Firly Putri Fardilla ◽  
Wiwit Ananda Wahyu Setyaningsih ◽  
...  
Keyword(s):  
Extracellular Matrix ◽  
Polymerase Chain Reaction ◽  
External Genitalia ◽  
Penile Curvature ◽  
Moderate Correlation ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Distal Hypospadias ◽  
Male External Genitalia ◽  
The Impact

Abstract Background Hypospadias, the most frequent congenital male external genitalia abnormality, is usually associated with curvature of the ventral penis, i.e. chordee. Abnormality of darto tissue has been suggested as the pathophysiology of chordees. Collagen is one of the most abundant fibrous proteins within the extracellular matrix. In this study, we determined the expression of collagen 1 (COL1A1) and COL6A1 in patients with hypospadias and associated them with the severity of penile curvature. Methods We included 60 children < 18 years old, consisting of 20 distal hypospadias, 20 proximal hypospadias patients, and 20 controls in our institution from 2017 – 2020. The expression of COL1A1 and COL6A1 in darto tissue was determined by reverse-transcriptase polymerase chain reaction (qPCR). The penile curvature severity was classified as mild (< 30 degrees), moderate (30–60 degrees), and severe (> 60 degrees). Results qPCR showed that COL1A1 and COL6A1 expression was significantly downregulated in the distal (0.88 (0.38–2.53) and 0.54 (0.16–4.35), respectively) and proximal 0.76 (0.33–2.57) and 0.57 (0.18–1.38), respectively) hypospadias groups compared to controls (1.85 (0.24–4.61) and 0.93 (0.17–4.06), respectively) with p-values of 0.024 and 0.018, respectively. Furthermore, there was a moderate correlation between COL1A1 and COL6A1 expression (r = 0.458, p < 0.0001). Interestingly, COL1A1 and COL6A1 were also significantly downregulated in the moderate and severe chordee groups compared to the mild chordee groups, with p-values of 0.003 and 0.037, respectively. Conclusions Aberrant COL1A1 and COL6A1 expression might affect abnormalities in darto tissue and penile curvature severity in hypospadias patients.

scholarly journals Digital PCR as an Emerging Tool for Monitoring of Microbial Biodegradation

Molecules ◽  
2020 ◽  
Vol 25 (3) ◽  
pp. 706 ◽  
Author(s):  
Yiqi Cao ◽  
Miao Yu ◽  
Guihua Dong ◽  
Bing Chen ◽  
Baiyu Zhang
Keyword(s):  
Digital Pcr ◽  
Absolute Quantification ◽  
Functional Genes ◽  
Chain Reaction ◽  
Real Time Quantitative Pcr ◽  
Quantification Method ◽  
Monitoring Technique ◽  
Microbial Biodegradation ◽  
Polymerase Chain ◽  
Pcr Techniques

Biodegradation of contaminants is extremely complicated due to unpredictable microbial behaviors. Monitoring of microbial biodegradation drives us to determine (1) the amounts of specific degrading microbes, (2) the abundance, and (3) expression level of relevant functional genes. To this endeavor, the cultivation independent polymerase chain reaction (PCR)-based monitoring technique develops from endpoint PCR, real-time quantitative PCR, and then into novel digital PCR. In this review, we introduce these three categories of PCR techniques and summarize the timely applications of digital PCR and its superiorities than qPCR for biodegradation monitoring. Digital PCR technique, emerging as the most accurately absolute quantification method, can serve as the most promising and robust tool for monitoring of microbial biodegradation.

scholarly journals A novel fluorescence quantification method for polymerase chain reaction system

2006 ◽  
Vol 266 (2) ◽  
pp. 744-750 ◽  
Author(s):  
Jui Hung Chien ◽  
Da Sheng Lee ◽  
Yi Ting Cheng ◽  
Shou Huei Yeh ◽  
Wen Ping Chou ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Reaction System ◽  
Chain Reaction ◽  
Polymerase Chain Reaction System ◽  
Quantification Method ◽  
Polymerase Chain

Mo1852 The Impact of Polymerase Chain Reaction on Clostridium difficile Detection and Clinical Outcomes

2015 ◽  
Vol 148 (4) ◽  
pp. S-726-S-727
Author(s):  
Mona Akbari ◽  
Victor Novack ◽  
Ciaran P. Kelly ◽  
Daniel A. Leffler
Keyword(s):  
Polymerase Chain Reaction ◽  
Clostridium Difficile ◽  
Clinical Outcomes ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
The Impact

scholarly journals Analysis of the impact of long non-coding RNA gene polymorphisms (ANRIL, MALAT1, HOTAIR) on some clinical and pathologic features in patients with bladder cancer

2021 ◽  
Vol 25 (2(98)) ◽  
pp. 13-21
Author(s):  
A. Volkohon ◽  
V. Harbuzova ◽  
I. Danilishin ◽  
D. Nechyporenko ◽  
O. Ataman
Keyword(s):  
Polymerase Chain Reaction ◽  
Real Time ◽  
Tumor Size ◽  
Transitional Cell ◽  
Polymorphism Analysis ◽  
Chain Reaction ◽  
Blood Hemoglobin ◽  
Pathologic Features ◽  
Polymerase Chain ◽  
The Impact

Objective – to analyze the possible association between the SNPs rs4977574 (ANRIL gene), rs3200401 (MALAT1 gene), rs1899663 (HOTAIR gene) and tumor size and some clinical and laboratory testing data in patients with transitional cell carcinoma of the urinary bladder (TCCUB).Material and methods. Whole venous blood of 141 patients with TCCUB was used. The genotyping of rs4977574 and rs3200401 sites was performed by real-time polymerase chain reaction (Real-time PCR). The rs1899663 locus genotyping was done by polymerase chain reaction followed by restriction fragment length polymorphism analysis (PCR-RFLP). Mathematical analysis of the obtained data was performed using the software package SPSS (version 17.0).Results. It was found that individuals with TT-genotype (rs3200401-polymorphism) have a lower blood hemoglobin content ((106.3 ± 23.9) g/l; P = 0.043) and higher blood glucose ((7.1 ± 2.3) mmol/l; P = 0.043) and creatinine ((104.5 ± 33.8) μmol/l; P = 0.022) than patients with CC genotype (respectively: (131.1 ± 21.9) g/l); (5.4 ± 1.5) mmol/l); (83.8 ± 18.5) μmol/l)). TT-homozygotes also have the higher tumor width ((4.2 ± 1.7) cm; P = 0.027) than in CC-homozygotes ((2.9 ± 1.1) cm). No significant association between rs4977574, rs1899663 loci and studied parameters was found.Conclusion. The MALAT1 gene rs3200401 polymorphism is associated with tumor size and blood hemoglobin, glucose, and creatinine levels in patients with TCCUB. No association between rs1899663, rs4977574 loci and clinical and pathological features in patients with TCUUB was detected.

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