MixtureFinder: Estimating DNA Mixture Models for Phylogenetic Analyses.

In phylogenetic studies, both partitioned models and mixture models are used to account for heterogeneity in molecular evolution among the sites of DNA sequence alignments. Partitioned models require the user to specify the grouping of sites into subsets, and then assume that each subset of sites can be modeled by a single common process. Mixture models do not require users to prespecify subsets of sites, and instead calculate the likelihood of every site under every model, while co-estimating the model weights and parameters.

Order of amino acid recruitment into the genetic code resolved by last universal common ancestor's protein domains.

The current "consensus" order in which amino acids were added to the genetic code is based on potentially biased criteria, such as the absence of sulfur-containing amino acids from the Urey-Miller experiment which lacked sulfur. More broadly, abiotic abundance might not reflect biotic abundance in the organisms in which the genetic code evolved. Here, we instead identify which protein domains date to the last universal common ancestor (LUCA) and then infer the order of recruitment from deviations of their ancestrally reconstructed amino acid frequencies from the still-ancient post-LUCA controls.

Study of Using Ultrasonic Waves in the Producing Dried Dragon Fruit Peel Processes.

In this study, ultrasound waves were successfully applied to the osmosis process of dried dragon fruit products. Additionally, this study was aimed at determining the suitable parameters for the process of drying dragon fruit peels. The parameters including the size of slices (2-5 cm), blanching time (10-25 min), ultrasonic time (10-25 min), ultrasonic temperature (45°C-60°C), ultrasonic power (100-250 W), and drying temperature (45°C-60°C) were fully investigated.

CMAPLE: Efficient Phylogenetic Inference in the Pandemic Era.

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.

Order of amino acid recruitment into the genetic code resolved by Last Universal Common Ancestor's protein domains.

The current "consensus" order in which amino acids were added to the genetic code is based on potentially biased criteria, such as absence of sulfur-containing amino acids from the Urey-Miller experiment which lacked sulfur. More broadly, abiotic abundance might not reflect biotic abundance in the organisms in which the genetic code evolved. Here, we instead identify which protein domains date to the last universal common ancestor (LUCA), then infer the order of recruitment from deviations of their ancestrally reconstructed amino acid frequencies from the still-ancient post-LUCA controls.

Multivariate Statistical Analysis for the Classification of Sausages Based on Physicochemical Attributes, Using Attenuated Total Reflectance-Fourier Transform Infrared (ATR-FTIR) and Inductively Coupled Plasma-Mass Spectrometry (ICP-MS).

Sausage is a convenient food that is widely consumed in the world and in Vietnam. Due to the rapid development of this product, the authenticity of many famous brands has faded by the rise of adulteration. Therefore, in this study, principal component analysis (PCA) was combined with chemical analysis to identify 6 sausage brands.

MAST: Phylogenetic Inference with Mixtures Across Sites and Trees.

Hundreds or thousands of loci are now routinely used in modern phylogenomic studies. Concatenation approaches to tree inference assume that there is a single topology for the entire dataset, but different loci may have different evolutionary histories due to incomplete lineage sorting (ILS), introgression, and/or horizontal gene transfer; even single loci may not be treelike due to recombination. To overcome this shortcoming, we introduce an implementation of a multi-tree mixture model that we call mixtures across sites and trees (MAST).

AliSim-HPC: parallel sequence simulator for phylogenetics.

Motivation: Sequence simulation plays a vital role in phylogenetics with many applications, such as evaluating phylogenetic methods, testing hypotheses, and generating training data for machine-learning applications. We recently introduced a new simulator for multiple sequence alignments called AliSim, which outperformed existing tools. However, with the increasing demands of simulating large data sets, AliSim is still slow due to its sequential implementation; for example, to simulate millions of sequence alignments, AliSim took several days or weeks.

DecentTree: scalable Neighbour-Joining for the genomic era.

Motivation: Neighbour-Joining is one of the most widely used distance-based phylogenetic inference methods. However, current implementations do not scale well for datasets with more than 10 000 sequences. Given the increasing pace of generating new sequence data, particularly in outbreaks of emerging diseases, and the already enormous existing databases of sequence data for which Neighbour-Joining is a useful approach, new implementations of existing methods are warranted.

Towards a Standardized Approach for the Geographical Traceability of Plant Foods Using Inductively Coupled Plasma Mass Spectrometry (ICP-MS) and Principal Component Analysis (PCA).

This paper presents a systematic literature review focused on the use of inductively coupled plasma mass spectrometry (ICP-MS) combined with PCA, a multivariate technique, for determining the geographical origin of plant foods. Recent studies selected and applied the ICP-MS analytical method and PCA in plant food geographical traceability. The collected results from many previous studies indicate that ICP-MS with PCA is a useful tool and is widely used for authenticating and certifying the geographic origin of plant food.

Maximum likelihood pandemic-scale phylogenetics.

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.

Atractylodes macrocephala Rhizomes Contain Anti-inflammatory Sesquiterpenes.

Two new compounds, named eudesm-4(15),7-diene-3α,9β,11-triol (1) and eudesm-4(15),7-diene-1β,3α,9β,11-tetraol (2) together with three known sesquiterpene lactones (1S,5R,7R,10R)-secoatractylolactone (3), (1S,5R,7R,10R)-secoatractylolactone-11-O-β-D-glucopyranoside (4) atractylenolide III (5) were isolated from the rhizomes of Atractylodes macrocephala. Their structures were elucidated by using one-dimensional (1D) and 2D-NMR spectra and high resolution electrospray ionization (HR-ESI)-MS data. Compound 5 exhibited the most active anti-inflammatory activity with IC values of 27.

Alpha-Glucosidase Inhibitory Activity of Saponins Isolated from Hance.

Species belonging to the (Asteraceae), the largest genus in the tribe Vernonieae (consisting of about 1,000 species), are widely used in food and medicine. These plants are rich sources of bioactive sesquiterpene lactones and steroid saponins, likely including many as yet undiscovered chemical components. A phytochemical investigation resulted in the separation of three new stigmastane-type steroidal saponins (1 - 3), designated as vernogratiosides A-C, from whole plants of .

Concentrations of polycyclic aromatic hydrocarbons in Vietnamese takeaway coffee: effects of coffee variety, roasting temperature and time.

The research goal was to estimate the level of risk to human health posed by polycyclic aromatic hydrocarbons (PAHs) in Vietnamese takeaway coffee. A variety of roasted coffee beans were collected and tested for the presence of PAHs in various takeaway locations throughout Vietnam. Furthermore, the effect of roasting conditions on PAH concentrations in Vietnamese Robusta coffee was also studied and demonstrated.

Updated site concordance factors minimize effects of homoplasy and taxon sampling.

Motivation: Site concordance factors (sCFs) have become a widely used way to summarize discordance in phylogenomic datasets. However, the original version of sCFs was calculated by sampling a quartet of tip taxa and then applying parsimony-based criteria for discordance. This approach has the potential to be strongly affected by multiple hits at a site (homoplasy), especially when substitution rates are high or taxa are not closely related.

Design of novel p-n heterojunction ZnBiO-ZnS photocatalysts with impressive photocatalytic and antibacterial activities under visible light.

Heterojunction structures have attracted considerable attention for enhancing electron migration across interfaces. In this report, ZnBiO-ZnS(12%) heterojunction photocatalysts was found to be capable of degrading over 94% of indigo carmine in a 15 mg/L solution within 90 min of visible light irradiation at a catalytic dose of 1.0 g/L and pH 4.

Maximum likelihood pandemic-scale phylogenetics.

Phylogenetics plays a crucial role in the interpretation of genomic data. Phylogenetic analyses of SARS-CoV-2 genomes have allowed the detailed study of the virus's origins, of its international and local spread, and of the emergence and reproductive success of new variants, among many applications. These analyses have been enabled by the unparalleled volumes of genome sequence data generated and employed to study and help contain the pandemic.

nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models.

Amino acid substitution models are a key component in phylogenetic analyses of protein sequences. All commonly used amino acid models available to date are time-reversible, an assumption designed for computational convenience but not for biological reality. Another significant downside to time-reversible models is that they do not allow inference of rooted trees without outgroups.

A Comprehensive Phylogenetic Analysis of the Serpin Superfamily.

Serine protease inhibitors (serpins) are found in all kingdoms of life and play essential roles in multiple physiological processes. Owing to the diversity of the superfamily, phylogenetic analysis is challenging and prokaryotic serpins have been speculated to have been acquired from Metazoa through horizontal gene transfer due to their unexpectedly high homology. Here, we have leveraged a structural alignment of diverse serpins to generate a comprehensive 6,000-sequence phylogeny that encompasses serpins from all kingdoms of life.

QMaker: Fast and Accurate Method to Estimate Empirical Models of Protein Evolution.

Amino acid substitution models play a crucial role in phylogenetic analyses. Maximum likelihood (ML) methods have been proposed to estimate amino acid substitution models; however, they are typically complicated and slow. In this article, we propose QMaker, a new ML method to estimate a general time-reversible $Q$ matrix from a large protein data set consisting of multiple sequence alignments.

Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression.

Our understanding of the evolutionary history of primates is undergoing continual revision due to ongoing genome sequencing efforts. Bolstered by growing fossil evidence, these data have led to increased acceptance of once controversial hypotheses regarding phylogenetic relationships, hybridization and introgression, and the biogeographical history of primate groups. Among these findings is a pattern of recent introgression between species within all major primate groups examined to date, though little is known about introgression deeper in time.