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Phylogenetics has a crucial role in genomic epidemiology. Enabled by unparalleled volumes of genome sequence data generated to study and help contain the COVID-19 pandemic, phylogenetic analyses of SARS-CoV-2 genomes have shed light on the virus's origins, spread, and the emergence and reproductive success of new variants. However, most phylogenetic approaches, including maximum likelihood and Bayesian methods, cannot scale to the size of the datasets from the current pandemic. We present 'MAximum Parsimonious Likelihood Estimation' (MAPLE), an approach for likelihood-based phylogenetic analysis of epidemiological genomic datasets at unprecedented scales. MAPLE infers SARS-CoV-2 phylogenies more accurately than existing maximum likelihood approaches while running up to thousands of times faster, and requiring at least 100 times less memory on large datasets. This extends the reach of genomic epidemiology, allowing the continued use of accurate phylogenetic, phylogeographic and phylodynamic analyses on datasets of millions of genomes.

Profile mixture models capture distinct biochemical constraints on the amino acid substitution process at different sites in proteins. These models feature a mixture of time-reversible models with a common matrix of exchangeabilities and distinct sets of equilibrium amino acid frequencies known as profiles. Combining the exchangeability matrix with each profile generates the matrix of instantaneous rates of amino acid exchange for that profile. Currently, empirically estimated exchangeability matrices (e.g. the LG matrix) are widely used for phylogenetic inference under profile mixture models. However, these were estimated using a single profile and are unlikely optimal for profile mixture models. Here, we describe the GTRpmix model that allows maximum likelihood estimation of a common exchangeability matrix under any profile mixture model. We show that exchangeability matrices estimated under profile mixture models differ from the LG matrix, dramatically improving model fit and topological estimation accuracy for empirical test cases. Because the GTRpmix model is computationally expensive, we provide two exchangeability matrices estimated from large concatenated phylogenomic-supermatrices to be used for phylogenetic analyses. One, called Eukaryotic Linked Mixture (ELM), is designed for phylogenetic analysis of proteins encoded by nuclear genomes of eukaryotes, and the other, Eukaryotic and Archaeal Linked mixture (EAL), for reconstructing relationships between eukaryotes and Archaea. These matrices, combined with profile mixture models, fit data better and have improved topology estimation relative to the LG matrix combined with the same mixture models. Starting with version 2.3.1, IQ-TREE2 allows users to estimate linked exchangeabilities (i.e. amino acid exchange rates) under profile mixture models. [ABSTRACT FROM AUTHOR]

Fingerprinting techniques, which utilize the unique chemical and physical properties of food samples, have emerged as a promising approach for food authentication and traceability. Recent studies have demonstrated significant advancements in food authentication through the use of fingerprinting methods, such as multivariate statistical analysis techniques applied to trace elements and isotope ratios. However, further research is required to optimize these methods and ensure their validity and reliability in real-world applications. In this study, the inductively coupled plasma mass spectrometry (ICP-MS) analytical method was employed to determine the content of 21 elements in 300 cashew nut (Anacardium occidentale L.) samples from 5 brands. Multivariate statistical methods, such as principal components analysis (PCA), were employed to analyze the data obtained and establish the provenance of the cashew nuts. While cashew nuts are widely marketed in many countries, no universal method has been utilized to differentiate the origin of these nuts. Our study represents the initial step in identifying the geographical origin of commercial cashew nuts marketed in Vietnam. The analysis showed significant differences in the means of 21 of the 40 analyzed elements among the cashew nut samples from the 5 brands, including 7Li, 11B, 24Mg, 27Al, 44Ca, 48Ti, 51V, 52Cr, 55Mn, 57Fe, 60Ni, 63Cu, 66Zn, 93Nb, 98Mo, 111Cd, 115In, 121Sb, 138Ba, 208Pb, and 209Bi. The PCA analysis indicated that the cashew nut samples can be accurately classified according to their original locations. This research serves as a prerequisite for future studies involving the combination of elemental composition analysis with statistical classification methods for the accurate establishment of cashew nut provenance, which involves the identification of key markers for the original discrimination of cashew nuts.

Ammonia-oxidising archaea (AOA) are ubiquitous and abundant in nature and play a major role in nitrogen cycling. AOA have been studied intensively based on the amoA gene (encoding ammonia monooxygenase subunit A), making it the most sequenced functional marker gene. Here, based on extensive phylogenetic and meta-data analyses of 33,378 curated archaeal amoA sequences, we define a highly resolved taxonomy and uncover global environmental patterns that challenge many earlier generalisations. Particularly, we show: (i) the global frequency of AOA is extremely uneven, with few clades dominating AOA diversity in most ecosystems; (ii) characterised AOA do not represent most predominant clades in nature, including soils and oceans; (iii) the functional role of the most prevalent environmental AOA clade remains unclear; and (iv) AOA harbour molecular signatures that possibly reflect phenotypic traits. Our work synthesises information from a decade of research and provides the first integrative framework to study AOA in a global context.

We have recently introduced MAPLE (MAximum Parsimonious Likelihood Estimation), a new pandemic-scale phylogenetic inference method exclusively designed for genomic epidemiology. In response to the need for enhancing MAPLE's performance and scalability, here we present two key components: (i) CMAPLE software, a highly optimized C++ reimplementation of MAPLE with many new features and advancements, and (ii) CMAPLE library, a suite of application programming interfaces to facilitate the integration of the CMAPLE algorithm into existing phylogenetic inference packages. Notably, we have successfully integrated CMAPLE into the widely used IQ-TREE 2 software, enabling its rapid adoption in the scientific community. These advancements serve as a vital step toward better preparedness for future pandemics, offering researchers powerful tools for large-scale pathogen genomic analysis. [ABSTRACT FROM AUTHOR]

Rapid urbanization has led to increased environmental pollution in Vietnam, especially air pollution issues. In this study, we used gas chromatography-mass spectrometry with an automated identification and quantification system database to detect and quantitate compounds in atmospheric fine particulate matter (PM2.5). A total of 288 compounds classified in 19 pollutant categories based on their origins were detected in PM2.5 samples collected in three areas of Hanoi during winter. The total content of substances detected ranged from 41.08 to 795.00 ng.m−3. The characteristics and concentrations of organic pollutants differed among the industrial, urban, and agricultural sampling areas, with average concentrations of 179.00, 112.10, and 529.40 ng.m−3, respectively. In this comprehensive study on trace organic compounds conducted with samples collected at three sites, we investigating the basic impact of three main factors on the environment. This study contributes to the literature by providing a data set on the content of trace organic substances in the air at the study site.

Partial shading conditions (PSC) have negative effects on the operation of photovoltaic (PV) systems. In this paper, a PV array reconfiguration method is developed to minimize power losses of PV arrays under partial shading conditions. The proposed reconfiguration method is based on equalizing the reduction of the short-circuit current of the PV modules in the PV array. Eight state-of-the-art Convolutional Neural Network models are employed to estimate the effect of shading on the short-circuit current of a PV module. These models include LeNet-5, AlexNet, VGG 11, VGG 19, Inception V3, ResNet 18, ResNet 34, and ResNet 50. Among eight models, the VGG 19 achieves the best accuracy on 1842 sample images. Therefore, this model is used to estimate the ratio of the actual short-circuit current and the estimated short-circuit current in four studied shading scenarios. This ratio decides the switching rule between PV modules throughout the PV array under PSC. A 2×2 experimental PV array shows that the proposed reconfiguration method improves the output power from 5.81% to 25.19% in four shading patterns. Accordingly, the power losses are reduced from 1.32% to 13.75%. The power improvement and the reduction of power losses of the proposed dynamic PV array reconfiguration system under four case studies demonstrates its effectiveness in addressing the effects of PSC on the PV array.

Inductively coupled plasma mass spectrometry (ICP-MS) analytical method was used to determine the content of 40 elements in 38 soybean samples (Glycine Max) from 4 countries. Multivariate statistical methods, such as principal components analysis (PCA), were performed to analyze the obtained data to establish the provenance of the soybeans. Although soybean is widely marketed in many countries, no universal method is used to discriminate the origin of these cereals. Our study introduced the initial step to the identification of the geographical origin of commercial soybean marketed in Vietnam. The analysis pointed out that there are significant differences in the mean of 33 of the 40 analyzed elements among 4 countries’ soybean samples, namely, 11B, 27Al, 44Ca, 45Sc, 47Ti, 55Mn, 56Fe, 59Co, 60Ni, 63Cu, 66Zn, 69Ga, 75As, 78Se, 85Rb, 88Sr, 89Y, 90Zr, 93Nb, 95Mo, 103Rh, 137Ba, 163Dy, 165Ho, 175Lu, 178Hf, 181Ta, 182W, 185Re, 197Au, 202Hg, 205Tl, and 208Pb. The PCA analysis showed that the soybean samples can be classified correctly according to their original locations. This research can be used as a prerequisite for future studies of using the combination of elemental composition analysis with statistical classification methods for an accurate provenance establishment of soybean, which determined a variation of key markers for the original discrimination of soybean.

Solid-based residues (SBRs) of Cordyceps militaris are often considered as waste after the cultivation of the fruiting body. To demonstrate the value of this by-product, different ratios of two favorable green solvents (EtOH and water) were employed to optimize the yields of cordycepin (Cor) and adenosine (Ado) and investigate relevant activities of plant growth inhibition (allelopathy), antioxidants, and xanthine oxidase. The SBR extracts of 60% EtOH-40% water (W4) and 40% EtOH-60% water (W6) exhibited the highest antioxidant activity as well as yielded the optimum content of Cor and Ado. The W4 and Wt (hot water) exhibited maximum inhibitory effects on the growth of Raphanus sativus (radish), Lactuca sativa (lettuce) and two noxious weeds, Echinochloa crus-galli (barnyard grass) and Bidens pilosa (beggarticks). Furthermore, GC-MS scan analysis revealed the presence of 14 major compounds in the SBRs. W4 is the best solvent to optimize yields of Cor and Ado, as well as having the strongest levels of antioxidant activity, xanthine oxidase, and growth-inhibitory activity. This study reveals that SBRs are a potential source of medicinal and agricultural utilization. [ABSTRACT FROM AUTHOR]