Variable Importance In Projection Analysis Research Articles

Expression Analysis of Phenylpropanoid Pathway Genes and Phenylpropanoid Accumulation in Different Organs of Chelidonium majus L.

Objective This study set out to examine the phenylpropanoid pathway gene expression and phenolic compound accumulation in different organs of Chelidonium majus (C. majus). Methods Total RNA was extracted and expression of phenylpropanoid biosynthesis genes was assessed using quantitative real-time polymerase chain reaction in different organs of C. majus. In addition, the phenylpropanoid compounds were analyzed from different organs of C. majus by using high-performance liquid chromatography. Results The results demonstrate the variance in the expression levels of phenylpropanoid pathway genes in the flowers, leaves, stems, and roots of C. majus. CmPAL and CmC4H were expressed at their greatest levels in the stem, while CmCHS and CmCHI were strongly expressed in the leaf, and CmF3H, CmFLS, Cm4CL, and CmDFR were more abundant in the flower. The total phenolic contents in the different organs also varied significantly. The highest value was recorded in the flowers (2152.89 ± 78.71 μg/g dry wt.), which was 54.26 times higher than the lowest values obtained from roots (39.68 ± 0.05 μg/g dry wt.). Except for roots, rutin showed the highest level in all other organs. According to a heat map, the majority of the phenolic compounds were highest in the flower. By using variable importance in projection analysis, the most significant metabolite was found to be chlorogenic acid, which had a positive association with all phenolic chemicals, but it showed a negative correlation with trans-cinnamic acid. Except for trans-cinnamic acid, all other phenolic compounds likewise showed positive correlation with other phenolic compounds. Conclusions This work offers pertinent data on the expression analysis of genes involved in the phenylpropanoid biosynthetic pathway and the presence of phenolic compounds in C. majus. These findings will be helpful for the researcher to understand the relationship between the expression level of phenylpropanoid pathway genes and phenylpropanoid compound accumulation in C. majus.

A serum metabolic biomarker panel for early rheumatoid arthritis.

There is an urgent need for novel biomarkers to improve the early diagnosis of rheumatoid arthritis (ERA). Current serum biomarkers used in the management of ERA, including rheumatoid factor and anti-cyclic citrullinated peptide (ACPA), show limited specificity and sensitivity. Here, we used metabolomics to uncover new serum biomarkers of ERA. We applied an untargeted metabolomics approach including gas chromatography time-of-flight mass spectrometry in serum samples from an ERA cohort (n=32) and healthy controls (n=19). Metabolite set enrichment analysis was performed to explore potentially important biological pathways. Partial least squares discriminant analysis and variable importance in projection analysis were performed to construct an ERA biomarker panel. Significant differences in the content of 11/81 serum metabolites were identified in patients with ERA. Receiver operating characteristic (ROC) analysis showed that a panel of only three metabolites (glyceric acid, lactic acid, and 3-hydroxisovaleric acid) could correctly classify 96.7% of patients with ERA, with an area under the ROC curve of 0.963 and with 94.4% specificity and 93.5% sensitivity, outperforming ACPA-based diagnosis by 2.9% and, thus, improving the preclinical detection of ERA. Aminoacyl-tRNA biosynthesis and serine, glycine, and phenylalanine metabolism were the most significant dysregulated pathways in patients with ERA. A metabolomics serum-based biomarker panel composed of glyceric acid, lactic acid, and 3-hydroxisovaleric acid offers potential for the early clinical diagnosis of RA.

Impact of varying levels of pasture allowance on the nutritional quality and functionality of milk throughout lactation

The objective of this study was to examine the impact of increasing proportions of grazed pasture in the diet on the composition, quality, and functionality of bovine milk across a full lactation. Fifty-four spring-calving cows were randomly assigned to 1 of 3 groups (n = 18), blocked on the basis of mean calving date (February 15, 2020 ± 0.8 d), pre-experimental daily milk yield (24.70 ± 3.70 kg), milk solids yield (2.30 ± 0.27 kg), lactation number (3.10 ± 0.13), and economic breeding index (182 ± 19). Raw milk samples were obtained weekly from each group between March and November 2020. Group 1 (GRS) consumed perennial ryegrass and was supplemented with 5% concentrates (dry matter basis); group 2 was maintained indoors and consumed a total mixed ration (TMR) diet consisting of maize silage, grass silage, and concentrates; and group 3 consumed a partial mixed ration diet (PMR), rotating between perennial ryegrass during the day and indoor TMR feeding at night. Raw milk samples consisted of a pooled morning and evening milking and were analyzed for gross composition, free amino acids, fatty acid composition, heat coagulation time, color, fat globule size, and pH. The TMR milks had a significantly higher total solids, lactose, protein, and whey protein as a proportion of protein content compared with both GRS and PMR milks. The GRS milks demonstrated a significantly lower somatic cell count (SCC), but a significantly higher pH and b*-value than both TMR and PMR milks. The PMR milks exhibited significantly lower total solids and fat content, but also demonstrated significantly higher SCC and total free amino acid content compared with GRS and TMR. Partial least squares discriminant analysis of fatty acid profiles displayed a distinct separation between GRS and TMR samples, while PMR displayed an overlap between both GRS and TMR groupings. Variable importance in projection analysis identified conjugated linoleic acid cis-9,trans-11, C18:2n-6 cis, C18:3n-3, C11:0, and C18:2n-6 trans as the largest contributors to the variation between the diets. Milk fats derived from GRS diets exhibited the highest proportion of unsaturated fats and higher unsaturation, health-promoting, and desaturase indices. The lowest proportions of saturated fats and the lowest atherogenic index were also exhibited by GRS-derived milk fats. This work highlights the positive influence of grass-fed milk for human consumption through its more nutritionally beneficial fatty acid profile, despite the highest milk solid percentages derived from TMR feeding systems. Furthermore, this study demonstrates the proportional response of previously highlighted biomarkers of pasture feeding to the proportion of pasture in the cow's diet.

Cost estimation for general aviation aircrafts using regression models and variable importance in projection analysis

Accurately estimating the development cost of general aviation aircraft plays a key role in devising the best strategy for corporates. However, studies on cost estimation for general aviation aircraft are limited. Development cost data of general aviation aircraft are commonly multi-collinear and the sample size is small, which may cause the estimation performance of the developed model to be poor. To address this issue, a combination of the variable importance in projection (VIP) analysis method and regression models is proposed. The VIP analysis method, applied to strong correlation data and small sample size, is utilized to select the most influential independent variables. The combined regression models tested using the selected variables include a partial least-squares regression (PLS) model and a back-propagation neural network (BPN) model. The PLS and BPN model are established respectively by utilizing the unfiltered raw variables for comparison. To verify the accuracy and feasibility of the proposed method, a case study utilizing general aviation aircraft cost data is presented. The results suggest that the VIP analysis method could be utilized for variable selection, and the proposed PLS model combined with VIP analysis has better prediction accuracy than that of the pure regression models and the combined BPN model, with MSE, MMRE, and R2 values of 1.07, 4.1% and 98.32%, respectively. Therefore, the VIP analysis method combined with the regression model can be effectively used to estimate the preliminary cost of general aviation aircraft. More importantly, this work provides a feasible method to improve the accuracy of cost estimation for general aviation aircraft.

In vivo Raman and autofluorescence study of the pigmented skin neoplasms

This paper studies classification of the pigmented skin neoplasms on the basis of the spectral Raman and autofluorescence features. The spectra registration was performed by means of the portable spectroscopic system with 785 nm laser radiation. The analysis of the spectral data was carried out using a projection on the latent structure with linear discriminant analysis. Using regression analysis the correlations between Raman and autofluorescence data were estimated. The variable importance in projection analysis allows one to find out important spectral information to differ spectra of the different neoplasm types. The use of combination of the Raman/autofluorescence data and projection method made it possible to classify pigmented skin neoplasms with 81% accuracy.

Correlations among flavor compounds, lipid oxidation indices, and endogenous enzyme activity during the processing of Xinjiang dry‐cured mutton ham

Mutton is widely consumed in China, European Mediterranean countries, and other regions around the world and is expected to gain popularity as an alternative to pork in dry-cured hams. Changes in the physicochemical indices, volatile compounds, and endogenous enzyme activities during the processing of dry-cured mutton ham were investigated. Eighty-six volatile compounds were identified during the dry-curing process, with aldehydes being dominant. Oxidation values increased significantly during dry-curing and decreased during ripening (p < .05). The activities of lipolytic enzymes remained active throughout processing, although the activities of the enzymes decreased. Lipoxidase activity increased rapidly during the fermenting stage and then decreased gradually during ripening (p < .05). Superoxide dismutase activity increased throughout processing, whereas the catalase activity decreased. According to partial least square variable importance in projection analysis, 49 odor-related compounds were selected from dry-cured mutton ham as specific compounds which are related to lipid oxidation and endogenous enzyme activities. Heatmap shows that the volatile compounds were correlated with enzyme activity and the oxidation value of dry-cured mutton ham during processing. Practical applications Xinjiang dry-cured mutton ham has an intense and a long-lasting aroma. Understanding the mechanism of aroma formation related to lipid oxidation could help us to improve the product quality and optimize the duration of processing. Therefore, the present work identified the characteristic flavor compounds and provided the changing regularity of these compounds at various stages to facilitate the generation of them.

Quantitative structure-property relationship study of cathode volume changes in lithium ion batteries using ab-initio and partial least squares analysis

In this paper, we report a method through the combination of ab-initio calculations and partial least squares (PLS) analysis to develop the Quantitative Structure –Activity Relationship (QSAR) formulations of cathode volume changes in lithium ion batteries. The PLS analysis is based on ab-initio calculation data of 14 oxide cathodes with spinel structure LiX2O4 and 14 oxide cathodes with layered-structure LiXO2 (X = Ti, V, Cr, Mn, Fe, Co, Ni, Nb, Mo, Ru, Rh, Pd, Ta, Ir). Five types of descriptors, describing the characteristics of each compound from crystal structure, element, composition, local distortion and electronic level, with 34 factors in total, are adopted to obtain the QSAR formulation. According to the variable importance in projection analysis, the radius of X4+ ion, and the X octahedron descriptors make major contributions to the volume change of cathode during delithiation. The analysis is hopefully applied to the virtual screening and combinatorial design of low-strain cathode materials for lithium ion batteries.

Non-targeted metabolomics of Brg1/Brm double-mutant cardiomyocytes reveals a novel role for SWI/SNF complexes in metabolic homeostasis.

Mammalian SWI/SNF chromatin-remodeling complexes utilize either BRG1 or Brm as alternative catalytic subunits to alter the position of nucleosomes and regulate gene expression. Genetic studies have demonstrated that SWI/SNF complexes are required during cardiac development and also protect against cardiovascular disease and cancer. However, Brm constitutive null mutants do not exhibit a cardiomyocyte phenotype and inducible Brg1 conditional mutations in cardiomyocyte do not demonstrate differences until stressed with transverse aortic constriction, where they exhibit a reduction in cardiac hypertrophy. We recently demonstrated the overlapping functions of Brm and Brg1 in vascular endothelial cells and sought here to test if this overlapping function occurred in cardiomyocytes. Brg1/Brm double mutants died within 21 days of severe cardiac dysfunction associated with glycogen accumulation and mitochondrial defects based on histological and ultrastructural analyses. To determine the underlying defects, we performed nontargeted metabolomics analysis of cardiac tissue by GC/MS from a line of Brg1/Brm double-mutant mice, which lack both Brg1 and Brm in cardiomyocytes in an inducible manner, and two groups of controls. Metabolites contributing most significantly to the differences between Brg1/Brm double-mutant and control-group hearts were then determined using the variable importance in projection analysis. Increased cardiac linoleic acid and oleic acid suggest alterations in fatty acid utilization or intake are perturbed in Brg1/Brm double mutants. Conversely, decreased glucose-6-phosphate, fructose-6-phosphate, and myoinositol suggest that glycolysis and glycogen formation are impaired. These novel metabolomics findings provide insight into SWI/SNF-regulated metabolic pathways and will guide mechanistic studies evaluating the role of SWI/SNF complexes in homeostasis and cardiovascular disease prevention.

Characterization of comprehensive appearances of skin ageing: An 11-year longitudinal study on facial skin ageing in Japanese females at Akita

Facial appearance is regarded as a typical index of ageing. However, people of the same age do not necessarily show the same degree of the facial appearance. The ageing of facial skin proceeds relatively slowly and therefore requires long-term follow-up to elucidate the mechanism of ageing changes. The purpose of this study was to identify facial skin parameters contributing the subjective impression of the overall ageing and characterize the degree of skin ageing by a 11 year longitudinal skin monitoring. One-hundred-eight healthy Japanese females excluded outside workers aged 5-64 at 1999, and lived in Akita, Japan till 2010 were enrolled. Facial images were collected to quantify various skin optical parameters. Skin colour, hydration and barrier function were measured with Chromameter, Corneometer and TEWAmeter, respectively. The visual evaluation of the overall facial skin ageing impression was also carried out. The skin parameters contributing visible impression of skin ageing were identified by variable importance in projection analysis, and the degree of facial skin ageing over 11 years was statistically classified by a cluster analysis. Facial skin parameters that comprehensively influenced visible skin ageing, including hyperpigmented spots, wrinkles and texture were studied. The Skin Ageing Score calculated from these three skin factors was used to classify the subjects into a mild, age-appropriate, and severe skin ageing group. The mild skin ageing group maintained significant better both skin optical and physical conditions. Variability and classification of the degree of facial skin ageing appearance were studied from this longitudinal research.