Results Of PCA Research Articles

The Important Role of TaohongSiwu Decoction in Gut Microbial Modulation in Response to High-Salt Diet-Induced Hypertensive Mice

TaohongSiwu decoction (THSWD), a traditional Chinese recipe, has been widely used to treat hypertension since ancient times. However, the mechanisms of its action are still unclear. Herein, we aimed to explore the gut microbial activity of THSWD in high-salt diet-induced hypertensive mice. Eight percent high-salt (NaCl) diet was used to induce hypertension for 4 weeks in a mouse model. Meanwhile, THSWD was used to intervene in the high-salt diet-induced mice, and the efficacy was evaluated by different parameters. Here, we found that THSWD significantly restored blood pressure compared with the model group. Moreover, THSWD effectively protected endothelial function by significantly upregulating the level of nitric oxide (NO) and downregulating the level of endothelin-1 (ET-1), angiotensin I (AngI), and vascular endothelial growth factor (VEGF) in serum compared with the model group. Notably, THSWD significantly upregulated the relative abundance of Dubosiella and downregulated that of Cyanobium_PCC-6307 and DNF00809 at the genus level compared with the model group. The results of PCA and microbial distance calculation further exhibited that THSWD treatment resulted in significant regulation of the microbial community. Furthermore, compared with the model group, THSWD increased the level of vitamin k2 (VK2) in serum. These findings indicate that THSWD could protect blood pressure and endothelial function by regulating gut microbiota and promoting microbial metabolite VK2. These results show the important role of THSWD in regulating the gut microbiota in response to high-salt diet-induced mice.

Farmers’ perspectives as determinants for adoption of conservation agriculture practices in Indo-Gangetic Plains of India

Understanding the farmer's perspective has traditionally been critical to influencing the adoption and out-scaling of CA-based climate-resilient practices. The objective of this study was to investigate the biophysical, socio-economic, and technical constraints in the adoption of CA by farmers in the Western- and Eastern-IGP, i.e., Karnal, Haryana, and Samastipur, Bihar, respectively. A pre-tested structured questionnaire was administered to 50 households practicing CA in Western- and Eastern-IGP. Smallholder farmers (<2 ha of landholding) in Karnal are 10% and Samastipur 66%. About 46% and 8% of households test soil periodically in Karnal and Samastipur, respectively. Results of PCA suggest economic profitability and soil health as core components from the farmer's motivational perspective in Karnal and Samastipur, respectively. Promotion and scaling up of CA technologies should be targeted per site-specific requirements, emphasizing biophysical resource availability, socio-economic constraints, and future impacts of such technology.

Fruit Phenolic and Triterpenic Composition of Progenies of Olea europaea subsp. cuspidata, an Interesting Phytochemical Source to Be Included in Olive Breeding Programs.

Olea europaea subsp. cuspidata has a relatively low commercial value due to the low size and pulp to stone ratio of its drupes compared to commercial olive cultivars. Nevertheless, this subspecies could represent a valid source of useful traits for olive breeding. In the current work, the drupe metabolic composition (secoiridoids, flavonoids, simple phenols, triterpenic acids, etc.) of a progeny of 27 cuspidata genotypes coming from free pollination and their female parent was evaluated by applying a powerful LC-MS method. A total of 62 compounds were detected within the profiles; 60 of them were annotated and 27 quantified. From a quantitative point of view, the genotypes from the progeny of cuspidata showed quite different metabolic profiles to olive common cultivars (“Arbequina”, “Frantoio”, “Koroneiki” and “Picual”) used as controls. Cuspidata drupes were richer in terms of several bioactive compounds such as rutin, hydroxytyrosol glucoside, a few interesting secoiridoids and the compounds of m/z 421 and 363. The relationships among several secondary metabolites determined in the progeny inferred from the results of both PCA and cross-correlation analysis were explained according to metabolic biosynthesis pathways in olive drupes. These outcomes underlined the potential of cuspidata genetic resources as a source of potentially interesting variability in olive breeding programs.

Fusion of Multi-Focus Images using Jellyfish Search Optimizer

When obtaining an image of a scene, the lens focuses on objects at a certain distance, and objects at other distances are blurred. This is called the limited depth of field problem. An approach for solving this problem is multi-focus image fusion. A clearer view of the entire scene is obtained by using the multi-focus image fusion method. For this method, at least two images captured at different focuses are combined. Various algorithms have been developed for multi-focus image fusion methods. For multi-focus image fusion, pixel-level block-based methods are commonly used. The block size is a factor that significantly affects the fusion performance. As a result, the block size parameter must be improved. The Jellyfish search optimization algorithm (JSA) is used to propose a block-based multi-focus image fusion approach based on the optimal selection of clearer image blocks from source images. The results of DWTPCA, DCHWT, APCA, PCA, SWTDWT and SWT methods, which are traditional image fusion methods, and ABC (artificial bee colony) and JSA optimization algorithms, which are metaheuristic methods, are compared. In addition, it has been determined that the JSA method has better performance than other traditional methods when compared both visually and quantitatively.

Genetic diversity analysis of Chinese fresh corn hybrids using SNP Chips

<p id="C3">China is a major fresh corn production and consumption country in the world. Assessment of genetic diversity and relationships among fresh corn hybrids in China has great benefit for hybrid identification and breed cultivation. In this study, an Illumina Maize 6K chip was employed to perform genome-wide scanning for the population structure and genetic distance of 385 fresh corn hybrids nationwide. The results showed that the average genetic diversity of 5067 SNP markers in 385 fresh corn hybrids was 0.406, with a range of 0.097-0.500. The average polymorphic information content (PIC) was 0.319, with a range of 0.092-0.375. The results of PCA and population genetic structure analysis revealed that the hybrids were mainly divided into three groups, which were non-sweet corn group (185 varieties), temperate sweet corn group (123 varieties), and tropical sweet corn group (77 varieties). The genetic distance between any two hybrids ranged from 0.132 to 0.472, with an average of 0.37. A total of 160 genome regions indicated strong population differentiation among different groups following <italic>F</italic>_ST analysis. Four key genes (<italic>sh2</italic>, <italic>su1</italic>, <italic>su2</italic>, and <italic>wx1</italic>) of starch synthesis pathway in maize grains were detected. Two candidate genes (<italic>sh2 </italic>and <italic>DGAT1-2</italic>) demonstrated different selection patterns in fresh corn groups and were validated using molecular markers. These results provide important theoretical guidance for the breeding and improvement of fresh corn varieties in China.

The Analysis of Correlations Between Terpene Transformations and Fermentation Type of Apple Musts

Abstract We measured the concentration of 13 terpenes in musts of 3 different apple cultivars fermented spontaneously, with Ethanol RED yeast (Saccharomyces cerevisiae) or Cider Yeast (Saccharomyces bayanus). Then we analysed obtained data with PCA with various packages in R to assess how different types of fermentation and apple cultivars affected terpene profile. The most informative results of PCA were obtained in ‘psych’ package and they indicated that there were groups of terpenes which concentrations increased simultaneously, while for some other groups the content of particular compounds was negatively correlated. This suggests that the first group of terpenes originated from different substrates while the latter group could be obtained from the same compound. Our findings indicated new possible pathways of terpene transformation, e.g. linalool, citral and geraniol could transform into one another. Moreover, the role of S. bayanus in those processes remains unclear and it requires further consideration.

Genetic Structure and Demographic History of Yellow Grouper (Epinephelus awoara) from the Coast of Southeastern Mainland China, Inferred by Mitochondrial, Nuclear and Microsatellite DNA Markers

The yellow grouper (Epinephelus awoara) is distributed in the West Pacific Ocean. Its genetic structure and demography were investigated using mitochondrial COI, Cyt b, the ND2 gene, the nuclear RyR3 gene, and 10 microsatellite DNA markers. A total of 120 individuals were collected from four locations along the coast of southeastern mainland China. High levels of haplotype diversity (0.968) were observed in mitochondrial DNA, and the average number of alleles ranged from 13.4 to 20.3 in microsatellite DNA data, which showed that all populations exhibited a high level of genetic diversity. Deficiency of heterozygosity was observed in all populations with positive FIS, showing that the characteristics of hermaphroditism might also be an underlying cause. The results of PCA, UPGMA clustering analysis and the significant genetic differentiation found in the Beibu Gulf population revealed the prevention of gene flow caused by the Qiongzhou Strait. The population of E. awoara also presented two major lineages, resulting in the appearance of the land bridge of the Taiwan Strait as a possible factor during the Pleistocene glaciation. Analysis of demographic history revealed that E. awoara underwent a reduction in effective population size in the past, followed by a single instantaneous increase in population size.

Analysis of the Fruit Quality of Pear (Pyrus spp.) Using Widely Targeted Metabolomics.

Pear is a kind of common temperate fruit, whose metabolite composition that contributes to the difference in fruit quality is unclear. This study identified and quantified the metabolites using a widely targeted LC-MS/MS approach in three pear species, including Pyrus bretschneideri (PB), Pyrus usssuriensis (PU) and Pyrus pyrifolia (PP). A total of 493 metabolites were identified, consisting of 68 carbohydrates, 47 organic acids, 50 polyphenols, 21 amino acids, 20 vitamins, etc. The results of PCA and OPLS-DA demonstrated that the metabolite compositions differed distinctly with cultivar variability. Our results also involved some metabolic pathways that may link to the fruit quality based on KEGG pathway analysis, the pathway of phenylalanine metabolism revealed significant differences between PB and PP (p < 0.05). Furthermore, the study selected D-xylose, formononetin, procyanidin A1 and β-nicotinamide mononucleotide as the major differentially expressed metabolites in the three species. The present study can open new avenues for explaining the differences in fruit quality of the major commercial pear cultivars in China.

Comparison of the Antioxidant Activity of Propolis Samples from Different Geographical Regions.

Propolis composition depends on several factors. The classification of propolis is based on its geographical location, color and agricultural characteristics. It is also classified according to the flora where the bees collect the resins, which represent the raw material for propolis production. Propolis possesses high antioxidant activity determined by its phenolic compounds. Due to diverse composition and possible impact on human health, eight samples of propolis were evaluated for their phenolic composition and antioxidant activity. Samples of Polish, Romanian, Turkish and Uruguayan origin propolis were used for phenolic spectrum determination using high performance liquid chromatography and photodiode array detection and in vitro DPPH and ABTS methods were used to determine the antioxidant activity of the extracts. PCA and HCA models were applied to evaluate the correlation between isolated polyphenols and antioxidant activity. The results confirmed variability in propolis composition depending on the geographical region of collection and the plant sources, and correlation between chemical composition and antioxidant activity. Results of PCA and HCA analyses confirm that Polish propolis is similar to that from different provinces of Romania, while Turkish and Uruguay are completely different. Polish and Romanian propolis belong to the poplar type. The assessed phenolic compounds of propolis samples used in the study are responsible for its antioxidant effect. The observed antioxidant activity of the analyzed samples may suggest directing subsequent research on prophylactic and therapeutic properties concerning cardiovascular, metabolic, neurodegenerative, and cancerous diseases, which are worth continuing.

Genetic diversity analysis of the wild edible mushroom Termitomyces heimii by using RAPD markers

To identify the genetic diversity of wild edible Termitomyces heimii (T. heimii) mushrooms, they were collected from three geographical locations in Baleswar, Kendujhar and Mayurbhanj districts in the North Odisha of India and were assessed using RAPD markers. 5 primers produced 43 scorable bands with 100% of the polymorphism. Polymorphic banding patterns with the number of amplified fragments varied from 6 (OPT 5 and OPT 12) to 11 (OPT 1) with an average of 8.6 per primer. The PIC values ranged from minimum value of 0.30 to maximum of 0.44 with an average value of 0.38. The heterozygosity (H) varied from 0.29 to 0.43 with an average of 0.36. The number of effective alleles (Ne), Shannon’s information index (I) and Nei’s gene diversity (h) were observed at population level as 1.604, 0.542 and 0.361 respectively whereas at species level the values were observed as 1.675, 0.684 and 0.459 respectively. These results showed the abundant genetic variability in the wild T. heimii. Nei’s gene diversity investigation showed that the genetic diversity was mainly found within geographical populations. The results of Mantel tests, UPGMA analysis, PCoA and PCA showed that geographical isolation is an important factor for the observed genetic differentiation.

Assessing growth performance and survival of wild shad Tenualosa ilisha fry in two earthen ponds with different feeding regime: A new insight for conservation

The present study describes the rearing and growth performance of Hilsa (Tenualosa ilisha) fry in experimental trial performed in earthen pond ecosystem located adjacent to river Rupnarayan for developing in-situ rearing protocol of fry collected from the wild sources. The seed was collected during May, 2020 from the river and stocked in two different rearing ponds. One of the ponds was provided with artificial feed and another fed with chicken offal to raise the production of zooplankton. Routine monitoring of water and soil quality parameters as well as other biotic communities like plankton was performed to understand the dynamics of ecological conditions in relation to changes in length and weight. The results of PCA between sediment quality and specific growth of fish indicated the strong positive loading of available nitrogen, available phosphate and free calcium carbonate, while moderate positive loading was observed with percentage of silt. Interestingly, it is observed that survivability rate of fish was approximately 80% in both the ponds. The results indicated natural growth fish was considerably well in both the experimental ponds. However, higher growth of juveniles were observed in the pond 2 with higher phytoplankton density (9120cells/L) than pond 1 having lower phytoplankton density (920cells/L) at the end of the experiments. The water quality parameters were comparable in both the experimental ponds. Based on this study it is evident that plankton (especially zooplankton) has induced better growth in pond 2 and possible incorporation of live feed along with formulated feed might trigger better growth of the stocked Hilsa. The present study provides new insight in developing field based approaches for successful rearing and conservation of threatened Hilsa in Indian waters.

Asymptotic Theory of Principal Component Analysis for Time Series Data with Cautionary Comments

AbstractPrincipal component analysis (PCA) is a most frequently used statistical tool in almost all branches of data science. However, like many other statistical tools, there is sometimes the risk of misuse or even abuse. In this paper, we highlight possible pitfalls in using the theoretical results of PCA based on the assumption of independent data when the data are time series. For the latter, we state with proof a central limit theorem of the eigenvalues and eigenvectors (loadings), give direct and bootstrap estimation of their asymptotic covariances, and assess their efficacy via simulation. Specifically, we pay attention to the proportion of variation, which decides the number of principal components (PCs), and the loadings, which help interpret the meaning of PCs. Our findings are that while the proportion of variation is quite robust to different dependence assumptions, the inference of PC loadings requires careful attention. We initiate and conclude our investigation with an empirical example on portfolio management, in which the PC loadings play a prominent role. It is given as a paradigm of correct usage of PCA for time series data.

Discrimination of the sister hedgehog species Erinaceus concolor and E. roumanicus(Erinaceomorpha: Mammalia): a geometric morphometric approach

This study investigates skull variation between the two closely related hedgehog species, Erinaceus concolor and E. roumanicus by using geometric morphometric analyses based on 2-dimensional landmarks. For this purpose, a total of 68 specimens were evaluated: 54 E. concolor and 14 E. roumanicus. The results of PCA, ANOVA and MANOVA analyses showed significant shape differences between the species, especially for the dorsal cranium. Shape differences were most prominent on the neurocranium and viscerocranium regions of the dorsal surface of the cranium and in mandibular ramus and the premolar regions. DFA tests were statistically significant against the null hypothesis of equal species means and crossvalidation scores were high enough to distinguish the species. Regression analyses also showed highly significant allometric differences between the two species, for both crania and mandibles. Finally, this study indicates that E. roumanicus is not only present in the European part of Turkey, but also in northwestern Anatolia.

Morphological Identification and DNA Barcoding of the Tropical Bed Bug Cimex hemipterus Fabricius (Hemiptera: Cimicidae) from Thrissur, Kerala, India

Knowledge of bed bugs is scant from Kerala due to improper identification, sparse population and better sanitation. But if an infestation begins it reaches extreme proportions because of the lack of awareness. To the best of our knowledge no detailed scientific studies on the identification of the bed bug species were carried out in Kerala. This study was aimed to perform morphological and molecular identification along with the morphometric analysis of the bed bug species from two sites—Avittappally and Mulankunnathukavu. Morphological identification was made by calculating the width to length ratios of the pronotum and hind femora. DNA barcoding was performed to identify the bed bug species accurately. A total of 21 morphological characters were used to compare bed bugs from the sample and the morphometric characters were measured and analysed using a Leica S8APO stereo microscope. The results indicated that the width-to-length ratios of pronotum and hind femora were 2.2±0.04 mm and 3.5±0.04 mm in Avittappally specimens and 2.1±0.05 mm and 3.2±0.05 mm in Mulankunnathukavu specimens. The genetic distance between the 2 COI sequence of our study were 0.027% and the intraspecific genetic distance between the 2 COI sequence of this study with 5 C. hemipterus sequences reported from other countries was found to be 0.025, 1.227, 0.058, 0.025 and 0.024% for Mulankunnathukavu specimen and 0.001, 1.280, 0.008, 0.001 and 0.001% for Avittappally specimen, respectively. The mean values of HL, HFW, HTW, MTW, FTW between the two places were significantly different. The results of PCA showed that the total percentage of variance reached 89.073% and 93.760%. Based on Morphological and morphometric characteristics along with molecular sequencing we assert that the bed bugs collected from both places were Cimex hemipterus.

The ligule ultrastructure of the tidal swamp rice (Oryza sativa) landraces of South Kalimantan, Indonesia, and their genetic diversity and relationship

Abstract. Mursyidin DH, Purnomo, Daryono BS. 2021. The ligule ultrastructure of the tidal swamp rice (Oryza sativa) landraces of South Kalimantan, Indonesia, and their genetic diversity and relationship. Biodiversitas 22: 5280-5285. In-depth characterization of rice landrace is needed in supporting the future conservation and crop breeding programs. Tidal swamp rice (Oryza sativa L.), belonging to this landrace, provided useful agronomic traits for both programs. In this study, the nine the tidal swamp rice ligule samples, mainly from South Kalimantan, Indonesia, were observed ultrastructurally using the SEM method. The diversity and relationships of this landrace based on the ligule ultrastructure were also determined using PCA and UPGMA methods. Generally the tidal swamp rice showed a unique ultrastructure of their ligule, composed of the large trichomes (prickle hair), small trichomes (micro hair), stomata-like structure, and silica cells, as well as the papillae that line along the veins. In this case, we found four patterns of the prickle hair on the ligule's abaxial surface, which has never been reported previously, namely scattered randomly, lined up on the vein, grid-step-like pattern, and unpatterned. The results of PCA and UPGMA showed that this landrace grouped into the same main three clusters, where Sardani (an outgroup) was included in the second cluster and joined with other cultivars from South Kalimantan. This information may be useful for the development of taxonomy and plant structures, and plant genetics and conservation.

Using multivariate statistical analysis in assessment of surface water quality and identification of heavy metal pollution sources in Sarough watershed, NW of Iran.

The Sarough watershed in NW Iran hosts a large amount of mineral occurrences and ore deposits which may be considered as the source of heavy metals in the region. The area has been studied previously; however, the methodology of this paper was less focused on previous studies. This study aimed to assess water quality, determine the spatial distribution pattern, and identify the sources of heavy metals in the main tributaries of Sarough watershed using pollution indexes, multivariate statistical methods, and processing data by geographic information system. Totally, 51 water samples were collected along the main rivers to determine the concentrations of heavy metals by ICP-MS. Regarding the drinking water, agriculture, and freshwater aquatic life guidelines, the rivers were assumed unsafe considering most of toxic elements' content, especially As. The mean values for heavy metal pollution indexes (HPI: 237.32) and metal indexes (MI: 25.37) indicated the intensive heavy metal pollution. The cluster analysis categorized the 51 sampling sites into four clusters with respect to pollution level. The results obtained from the Kruskal-Wallis and multiple comparison tests had the harmony with the results of CA in introducing the most impacted sampling sites and the parameters responsible for water quality degradation. The results of PCA showed the maximum similarity between As, Sb, Se, Fe, and Mn as well as base metals which was attributed to anthropogenic input from mining and mineral processing wastes. Association of Cr and Ni may suggest a lithology source (weathering of metamorphosed ultramafic outcrops). The maps prepared in the GIS system showed the spatial distribution pattern of toxic elements with maximum values nearby mining sites which decreases gradually toward downstream areas. Finally, the results showed that the Sarough River and its tributaries are influenced by high concentrations of heavy metals from the drainages of mining and ore processing sites and naturally occurring metal loadings as well as the geogenic sources such as weathering of geologic formations and hot springs.

Analysis of volatile flavor compounds of green wheat under different treatments by GC-MS and GC-IMS.

Volatile components in green wheat under different treatments including raw, washing, blanching, precooling, freezing, steaming, boiling, frying, and freeze-drying were evaluated by gas chromatography-ion mobility spectroscopy (GC-IMS) and gas chromatography-mass spectrometry (GC-MS). Five key aroma substances including n-hexanal, benzaldehyde, nonanal, 2-pentylfuran, and (E)-oct-2-enal were found by Venn diagram and odor activity values (OAV). Furthermore, according to volatile fingerprints characteristics and the aroma profile of sensory evaluation, it was found that green wheat under different treatments mainly presented seven characteristic flavor notes including sweet flowers, fat fragrance, mushroom hay, waxy aldehyde, citrus fruity, vegetable-like bean, and bitter almond from the sensory evaluation, and they could be divided into four categories, which was consistent with the results of PCA and GC-IMS. Hence, the volatile compounds of green wheat samples could be visualized and identified quickly via GC-IMS and the samples could be clearly classified based on the difference of volatile compounds. PRACTICAL APPLICATIONS: In the study, fingerprints coupled with cluster analysis were a visualized method for the identification of volatile compounds. Meanwhile, a new method, Venn diagram with OAV, was used to identify the key aroma of products. Finally, a rapid method to classify products by GC-IMS was performed. In future practical applications, GC-IMS can be used to classify products from different origins and different manufacturers. Similarly, it can identify fake and inferior products and whether the products have deteriorated. In addition, this research will provide a new strategy to find the relationship between flavor compounds and various processed technologies toward different cereals.

Genetic divergence and interrelationships for yield and yield attributing traits in horsegram

The present experiment was carried out to estimate the genetic diversity by cluster and Principal Component analyses for seven yield and yield attributing traits in 50 horse gram germplasm accessions and two checks during the late kharif, 2019. In correlation analysis, the grain yield was positively and significantly associated with test weight and number of pods which suggested the possibilities of improving grain yield by simultaneous improvement of these traits. Using cluster analysis, the accessions were grouped into five clusters. Based on the average cluster mean, the first cluster had high mean values for grain yield, the number of pods, test weight and plant height. The results of PCA revealed that, PC1, PC2, PC3 having eigenvalue greater than 1 contributed to the total variability of 82.69 per cent. Horse gram genetic improvement is receiving less attention from researchers across the globe. Using the results of this study, there is a tremendous space for genetic enhancement in grain yield of horsegram. Key wordsGenetic divergence, PCA, Correlation, Eigenvalue, Horsegram

Decortication induced changes in the physico-chemical, anti-nutrient, and functional properties of sorghum

The milling characteristics, physico-chemical properties, nutrient, and functional characteristics of sorghum were evaluated following field-level abrasive decortication to ascertain the impact of polishing parameters. Both grain moisture content and polishing time were found to significantly influence the degree of polish, endosperm yield, percentage broken, grain hardness, and thousand-grain weight. Both the proximate composition and mineral content of the flour decreased owing to decortication, indicating their dominant presence in the bran fractions. A more significant reduction in tannins was observed as compared to phytates meaning that phytates might be more localized in the inner layers, and tannins are majorly concentrated in the outer grain portions. Whole grain flour possessed better water and oil absorption capacities and lower bulk density value compared to polished fractions. There was also an increase in L* (lightness) and decrease in a* (red to green) and b* (yellow to blue) values in the polished flour samples indicating that decortication results in an overall improvement of the color of refined fractions. Results of PCA suggested a significant correlation between certain components namely fibre contents and tannin, ash content and mineral contents, and fibre and water absorption capacity, signifying that they co-vary with respect to one another. The cluster analysis suggested the importance of selected variables and their impact on the responses, as a clear demarcation was seen in the samples obtained from raw and polished grains.

Plasmonic Carbonaceous Nanotemplates for Microplastics Raman Detection

Plasmonic Carbonaceous Nanotemplates for Microplastics Raman Detection