Principal Component Analysis

Gewers, Felipe L.; Ferreira, Gustavo Rodrigues; Arruda, Henrique Ferraz de; Silva, Filipi N.; Comin, César H.; Amancio, Diego R.; Costa, Luciano da Fontoura

doi:10.1145/3447755

Cited by 182 publications

(67 citation statements)

References 46 publications

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“…Principal component analysis (PCA) is commonly used to analyze diverse data, particularly for the purposes of dimensionality reduction and visualization [ 38 ]. Here, the 60 VOCs detected in the pepper samples at the four developmental periods were formed into a 4 × 60 matrix for principal component analysis.…”

Section: Resultsmentioning

confidence: 99%

Effects of Cabya (Piper retrofractum Vahl.) Fruit Developmental Stage on VOCs

Wang

Fan

Zhong

et al. 2022

Foods

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The differences in VOCs can affect the flavor and medicinal value of cabya, and the flavor changes that occur in stages as the fruit develops are currently unknown. In order to investigate the influence of the developmental stage on the aroma composition of cabya essential oil, VOCs at each of the four developmental stages were analyzed by steam distillation (SD) extraction combined with GC-MS detection. The similarities and differences in fruit composition among the developmental stages were evaluated using hierarchical cluster analysis (HCA) and principal component analysis (PCA). A total of 60 VOCs, mainly alcohols, alkenes and alkanes, were identified across all of the developmental stages. The most acidic substances were detected in phase A and have a high medicinal value. There was no significant difference between the B and C phases, and the alcohols in those phases mainly promoted terpenoid synthesis in the D phase. Constituents during the D phase were mainly alkenes, at 57.14%, which contributed significantly to the aroma of the essential oil. PCA and HCA both were able to effectively differentiate the cabya fruit developmental stages based on the SD-GC-MS data. In summary, this study investigated the flavor variation characteristics and the diversity of VOCs in cabya fruits at different developmental stages, and its findings can provide a reference for developing essential oil products for different uses and determining appropriate stages for harvesting cabya resources.

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Section: Resultsmentioning

confidence: 99%

Effects of Cabya (Piper retrofractum Vahl.) Fruit Developmental Stage on VOCs

Wang

Fan

Zhong

et al. 2022

Foods

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“…The eigenvalues are distributed intensively on the axis, and the abnormal eigenvalues easily deviate from the axis. Deviation from the axis is an important basis for PCA to detect outliers [ 56 ].…”

Section: Methodsmentioning

confidence: 99%

Protected Geographical Indication Discrimination of Zhejiang and Non-Zhejiang Ophiopogonis japonicus by Near-Infrared (NIR) Spectroscopy Combined with Chemometrics: The Influence of Different Stoichiometric and Spectrogram Pretreatment Methods

et al. 2023

Molecules

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This paper presents a method for the protected geographical indication discrimination of Ophiopogon japonicus from Zhejiang and elsewhere using near-infrared (NIR) spectroscopy combined with chemometrics. A total of 3657 Ophiopogon japonicus samples from five major production areas in China were analyzed by NIR spectroscopy, and divided into 2127 from Zhejiang and 1530 from other areas (‘non-Zhejiang’). Principal component analysis (PCA) was selected to screen outliers and eliminate them. Monte Carlo cross validation (MCCV) was introduced to divide the training set and test set according to a ratio of 3:7. The raw spectra were preprocessed by nine single and partial combination methods such as the standard normal variable (SNV) and derivative, and then modeled by partial least squares regression (PLSR), a support vector machine (SVM), and soft independent modeling of class analogies (SIMCA). The effects of different pretreatment and chemometrics methods on the model are discussed. The results showed that the three pattern recognition methods were effective in geographical origin tracing, and selecting the appropriate preprocessing method could improve the traceability accuracy. The accuracy of PLSR after the standard normal variable was better, with R2 reaching 0.9979, while that of the second derivative was the lowest with an R2 of 0.9656. After the SNV pretreatment, the accuracy of the training set and test set of SVM reached the highest values, which were 99.73% and 98.40%, respectively. The accuracy of SIMCA pretreated with SNV and MSC was the highest for the origin traceability of Ophiopogon japonicus, which could reach 100%. The distance between the two classification models of SIMCA-SNV and SIMCA-MSC is greater than 3, indicating that the SIMCA model has good performance.

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“…(1) Data standardization—normalization method [ 67 ]

where

is the binding-energy value of normalized rubber and toxic receptor,

is the original binding-energy value of rubber and toxic receptor, and

is the L2 norm of the row vectors of the three toxicity numerical matrices.…”

Section: Methodsmentioning

confidence: 99%

Exploring the Potential Hormonal Effects of Tire Polymers (TPs) on Different Species Based on a Theoretical Computational Approach

Wang

Yang

et al. 2023

Polymers

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Tire polymers (TPs) are the most prevalent type of microplastics and are of great concern due to their potential environmental risks. This study aims to determine the toxicity of TPs with the help of molecular-dynamics simulations of their interactions with receptors and to highlight the differences in the toxicity characteristics of TPs in different environmental media (marine environment, freshwater environment, soil environment). For this purpose, five TPs—natural rubber, styrene–butadiene rubber (SBR), butadiene rubber, nitrile–butadiene rubber, and isobutylene–isoprene rubber—were analyzed. Molecular-dynamics calculations were conducted on their binding energies to neurotoxic, developmental, and reproductive receptors of various organisms to characterize the toxic effects of the five TPs. The organisms included freshwater species (freshwater nematodes, snails, shrimp, and freshwater fish), marine species (marine nematodes, mussels, crab, and marine fish), and soil species (soil nematodes, springtails, earthworms, and spiders). A multilevel empowerment method was used to determine the bio-toxicity of the TPs in various environmental media. A coupled-normalization method–principal-component analysis–factor-analysis weighting method—was used to calculate the weights of the TP toxicity (first level) categories. The results revealed that the TPs were the most biologically neurotoxic to three environmental media (20.79% and 10.57% higher compared with developmental and reproductive toxicity, respectively). Regarding the effects of TPs on organisms in various environmental media (second level), using a subjective empowerment approach, a gradual increase in toxicity was observed with increasing trophic levels due to the enrichment of TPs and the feeding behavior of organisms. TPs had the greatest influence in the freshwater-environment organisms according to the subjective empowerment approach employed to weight the three environmental media (third level). Therefore, using the minimum-value method coupled with the feature-aggregation method, the interval-deflation method coupled with the entropy-weighting method, and the standard-deviation normalization method, the three toxicity characteristics of SBR in three environmental media and four organisms were determined. SBR was found to have the greatest impact on the overall toxicity of the freshwater environment (12.38% and 9.33% higher than the marine and soil environments, respectively). The greatest contribution to neurotoxicity (26.01% and 15.95% higher than developmental and reproductive toxicity, respectively) and the greatest impact on snails and shrimp among organisms in the freshwater environment were observed. The causes of the heterogeneity of SBR’s toxicity were elucidated using amino-acid-residue analysis. SBR primarily interacted with toxic receptors through van der Waals, hydrophobic, π-π, and π-sigma interactions, and the more stable the binding, the more toxic the effect. The toxicity characteristics of TMPs to various organisms in different environments identified in this paper provide a theoretical basis for subsequent studies on the prevention and control of TMPs in the environment.

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Principal Component Analysis

Cited by 182 publications

References 46 publications

Effects of Cabya (Piper retrofractum Vahl.) Fruit Developmental Stage on VOCs

Effects of Cabya (Piper retrofractum Vahl.) Fruit Developmental Stage on VOCs

Protected Geographical Indication Discrimination of Zhejiang and Non-Zhejiang Ophiopogonis japonicus by Near-Infrared (NIR) Spectroscopy Combined with Chemometrics: The Influence of Different Stoichiometric and Spectrogram Pretreatment Methods

Exploring the Potential Hormonal Effects of Tire Polymers (TPs) on Different Species Based on a Theoretical Computational Approach

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