Search Results (3)

Semi-covariance has attracted significant attention in recent years and is increasingly employed to elucidate statistical phenomena exhibiting fluctuations, such as the similarity or difference in charge patterns of spike proteins among coronaviruses. In this study, by examining values above and below the average/mean based on the positive and negative charge patterns of amino acid residues in the spike proteins of SARS-CoV-2 and its current circulating variants, the proposed methods offer profound insights into the nonlinear evolving trends in those viral spike proteins. Our study indicates that the charge span value can predict the infectivity of the virus and the charge density can estimate the virulence of the virus, and both predicated infectivity and virulence appear to be associated with the capability of viral immune escape. This semi-covariance coefficient analysis may be used not only to predict the infectivity, virulence and capability of immune escape for coronaviruses but also to analyze the functionality of other viral proteins. This study improves our understanding of the trend of viral evolution in terms of viral infectivity, virulence or the capability of immune escape, which remains further validated by more future studies and statistical data. Full article

The rapid acquisition of high-resolution spatial distribution of soil organic matter (SOM) at the field scale is essential for precision agriculture. The UAV imaging hyperspectral technology, with its high spatial resolution and timeliness, can fill the research gap between ground-based monitoring and remote sensing. This study aimed to test the feasibility of using UAV hyperspectral data (400–1000 nm) with a small-sized calibration sample set for mapping SOM at a 1 m resolution in typical low-relief black soil areas of Northeast China. The experiment was conducted in an approximately 20 ha field. For calibration, 20 samples were collected using a 100 × 100 m grid sampling strategy, while 20 samples were randomly collected for independent validation. UAV captured hyperspectral images with a spatial resolution of 0.05 × 0.05 m. The extracted spectra within every 1 × 1 m were then averaged to represent the spectra of that grid; this procedure was also performed across the whole field. Upon applying various spectral pretreatments, including absorbance conversion, multiple scattering correction, Savitzky–Golay smoothing filtering, and first-order differentiation, the absolute maximum values of the correlation coefficients of the spectra for SOM increased from 0.41 to 0.58. Importance analysis from the optimal random forest (RF) model showed that the characterized bands of SOM were located in the 450–600 and 750–900 nm regions. When the RF model was used, the UAV hyperspectra data (UAV-RF) were able to successfully predict SOM, with an R² of 0.53 and RMSE of 1.48 g kg⁻¹. The prediction accuracy was then compared with that obtained using ordinary kriging (OK) and the RF model based on proximal sensing (PS-RF) with the same number of calibration samples. However, the OK method failed to predict the SOM accuracy (RMSE = 2.17 g kg⁻¹; R² = 0.02) due to a low sampling density. The semi-covariance function was unable to describe the spatial variability of SOM effectively. When the sampling density was increased to 50 × 50 m, OK successfully predicted SOM, with RMSE = 1.37 g kg⁻¹ and R² = 0.59, and its results were comparable to those of UAV-RF. The prediction accuracy of PS-RF was generally consistent with that of UAV-RF, with RMSE values of 1.41 g kg⁻¹ and 1.48 g kg⁻¹ and R² values of 0.57 and 0.53, respectively, which indicated that SOM prediction based on UAV-RF is feasible. Additionally, compared with the PS platforms, the UAV hyperspectral technology could simultaneously provide spectral information of tens or even hundreds of continuous bands and spatial information at the same time. This study provides a reference for further research and development of UAV hyperspectral techniques for fine-scale SOM mapping using a small number of samples. Full article

Complex modeling has received significant attention in recent years and is increasingly used to explain statistical phenomena with increasing and decreasing fluctuations, such as the similarity or difference of spike protein charge patterns of coronaviruses. Different from the existing covariance or correlation coefficient methods in traditional integer dimension construction, this study proposes a simplified novel fractional dimension derivation with the exact Excel tool algorithm. It involves the fractional center moment extension to covariance, which results in a complex covariance coefficient that is better than the Pearson correlation coefficient, in the sense that the nonlinearity relationship can be further depicted. The spike protein sequences of coronaviruses were obtained from the GenBank and GISAID databases, including the coronaviruses from pangolin, bat, canine, swine (three variants), feline, tiger, SARS-CoV-1, MERS, and SARS-CoV-2 (including the strains from Wuhan, Beijing, New York, German, and the UK variant B.1.1.7) which were used as the representative examples in this study. By examining the values above and below the average/mean based on the positive and negative charge patterns of the amino acid residues of the spike proteins from coronaviruses, the proposed algorithm provides deep insights into the nonlinear evolving trends of spike proteins for understanding the viral evolution and identifying the protein characteristics associated with viral fatality. The calculation results demonstrate that the complex covariance coefficient analyzed by this algorithm is capable of distinguishing the subtle nonlinear differences in the spike protein charge patterns with reference to Wuhan strain SARS-CoV-2, which the Pearson correlation coefficient may overlook. Our analysis reveals the unique convergent (positive correlative) to divergent (negative correlative) domain center positions of each virus. The convergent or conserved region may be critical to the viral stability or viability; while the divergent region is highly variable between coronaviruses, suggesting high frequency of mutations in this region. The analyses show that the conserved center region of SARS-CoV-1 spike protein is located at amino acid residues 900, but shifted to the amino acid residues 700 in MERS spike protein, and then to amino acid residues 600 in SARS-COV-2 spike protein, indicating the evolution of the coronaviruses. Interestingly, the conserved center region of the spike protein in SARS-COV-2 variant B.1.1.7 shifted back to amino acid residues 700, suggesting this variant is more virulent than the original SARS-COV-2 strain. Another important characteristic our study reveals is that the distance between the divergent mean and the maximal divergent point in each of the viruses (MERS > SARS-CoV-1 > SARS-CoV-2) is proportional to viral fatality rate. This algorithm may help to understand and analyze the evolving trends and critical characteristics of SARS-COV-2 variants, other coronaviral proteins and viruses. Full article