Comparison Of Methods
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Eliška Čermáková ◽  
Kamila Zdeňková ◽  
Kateřina Demnerová ◽  
Jaroslava Ovesná

The success of polymerase chain reaction (PCR) assay depends on template deoxyribonucleic acid (DNA) being sufficient with respect to both quantity and quality. Some biological materials contain compounds which inhibit the functioning of DNA polymerase and thus need to be removed as part of the DNA extraction procedure. The aim of the present experiments was to optimise the process of DNA isolation from various types of black, fruit and herbal teas. A comparison was made between two cetyltrimethylammonium bromide (CTAB)-based protocols and two commercially available DNA purification kits. The yield and integrity of the extracted DNA were monitored both spectrophotometrically and using agarose gel electrophoresis. The presence/absence of inhibitors in the DNA preparations was checked by running quantitative real-time PCRs. The optimal protocol was deemed to be the CTAB method described in ISO 21571:2005, so this method is recommended for the routine sample analysis of tea products.

2021 ◽  
pp. e01011
Josoa R. Randriamalala ◽  
Maholisoa Randrianomana ◽  
Rado E. Ranaivoson ◽  
Zo H. Rabemananjara ◽  
Dominique Hervé

2021 ◽  
Danielle Fahey ◽  
Mila Tasseva-Kurktchieva

Cognates, words with overlapping form and meaning, are used extensively in psycholinguistic investigations of bilingual processing. Previous research varied in the use of different qualitative and quantitative descriptions of cognates. Definitions have relied upon researchers’ perceptions, and decisions on cognate status have been defined by scores from either bilingual perceptual data or theoretical cross-linguistic differences. To determine which theoretical method for comparison most closely aligns with perceptual ratings of spoken words, we asked Spanish-English bilinguals to rate the similarity of sets of cognate pairs they heard. Rating scores were compared to 5 quantitative methods: standard methods such as orthographic and IPA Levenshtein distances, Van Orden’s, and Weber’s; plus, a novel method weighting phonological features. Comparisons of methods showed that orthographic differences were more predictive than phonological differences, suggesting that orthographic comparison methods are valid, and that orthographic representations are activated during auditory processing.

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0257633
Sanoji Wijenayake ◽  
Shafinaz Eisha ◽  
Zoya Tawhidi ◽  
Michael A. Pitino ◽  
Michael A. Steele ◽  

Milk is a highly complex, heterogeneous biological fluid that contains non-nutritive, bioactive extracellular vesicles called exosomes. Characterization of milk-derived exosomes (MDEs) is challenging due to the lack of standardized methods that are currently being used for milk pre-processing, storage, and exosome isolation. In this study, we tested: 1) three pre-processing methods to remove cream, fat, cellular debris, and casein proteins from bovine milk to determine whether pre-processing of whole milk prior to long-term storage improves MDE isolations, 2) the suitability of two standard exosome isolation methods for MDE fractionation, and 3) four extraction protocols for obtaining high quality RNA from bovine and human MDEs. MDEs were characterized via Transmission Electron Microscopy (TEM), Nanoparticle Tracking Analysis (NTA), and western immunoblotting for CD9, CD63, and Calnexin protein markers. We also present an optimized method of TEM sample preparation for MDEs. Our results indicate that: 1) Removal of cream and fat globules from unpasteurized bovine milk, prior to long-term storage, improves the MDE yield but not purity, 2) Differential ultracentrifugation (DUC) combined with serial filtration is better suited for bovine MDE isolation compared to ExoQuick (EQ) combined with serial filtration, however both methods were comparable for human milk, and 3) TRIzol LS is better suited for RNA extraction from bovine MDEs isolated by EQ and DUC methods. 4) TRIzol LS, TRIzol+RNA Clean and Concentrator, and TRIzol LS+RNA Clean and Concentrator methods can be used for RNA extractions from human MDEs isolated by EQ, yet the TRIzol LS method is better suited for human MDEs isolated by DUC. The QIAzol + miRNeasy Mini Kit produced the lowest RNA yield for bovine and human MDEs.

Natalia ANUFRİEVA ◽  
Semyon LİMANOV ◽  
Natalia ANCHUTİNA ◽  
Maria Kats KATS

2021 ◽  
Delin Sun ◽  
Gopalkumar Rakesh ◽  
Emily K. Clarke-Rubright ◽  
Courtney C. Haswell ◽  
Mark Logue ◽  

Results of neuroimaging datasets aggregated from multiple sites may be biased by site-specific profiles in participants demographic and clinical characteristics, as well as MRI acquisition protocols and scanning platforms. We compared the impact of four different harmonization methods on results obtained from analyses of cortical thickness data: (1) linear mixed-effects model (LME) that models site-specific random intercepts (LMEINT), (2) LME that models both site-specific random intercepts and age-related random slopes (LMEINT+SLP), (3) ComBat, and (4) ComBat with a generalized additive model (ComBat-GAM). Our test case for comparing harmonization methods was cortical thickness data aggregated from 29 sites, which included 1,343 cases with posttraumatic stress disorder (PTSD) (6.2-81.8 years old) and 2,067 trauma-exposed controls without PTSD (6.3-85.2 years old). We found that, compared to the other data harmonization methods, data processed with ComBat-GAM were more sensitive to the detection of significant case-control differences in regional cortical thickness (Chi2(3) = 34.339, p < 0.001), and case-control differences in age-related cortical thinning (Chi2(3) = 15.128, p = 0.002). Specifically, ComBat-GAM led to larger effect size estimates of cortical thickness reductions (corrected p-values < 0.001), smaller age-appropriate declines (corrected p-values < 0.001), and lower female to male contrast (corrected p-values < 0.001) in cases compared to controls relative to other harmonization methods. Harmonization with ComBat-GAM also led to greater estimates of age-related declines in cortical thickness (corrected p-values < 0.001) in both cases and controls compared to other harmonization methods. Our results support the use of ComBat-GAM for harmonizing cortical thickness data aggregated from multiple sites and scanners to minimize confounds and increase statistical power.

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