Efficient inference of large prokaryotic pangenomes with PanTA

Pangenome inference is an indispensable step in bacterial genomics, yet its scalability poses a challenge due to the rapid growth of genomic collections. This paper presents PanTA, a software package designed for constructing pangenomes of large bacterial datasets, showing unprecedented efficiency levels multiple times higher than existing tools. PanTA introduces a novel mechanism to construct the pangenome progressively without rebuilding the accumulated collection from scratch. The progressive mode is shown to consume orders of magnitude less computational resources than existing solutions in managing growing datasets. The software is open source and is publicly available at https://github.com/amromics/panta and at 10.6084/m9.figshare.23724705

ANTECEDENTS OF TOURISTS’ LOYALTY: THE ROLE AND INFLUENCE OF TOURISM PRODUCTS, DESTINATION IMAGE IN HOIAN WORLD CULTURAL HERITAGE SITE

The study’s aim is to examine the antecedents of destination loyalty, and considers the role and influence of tourism products and destination image to international tourisms’ loyalty in case of HoiAn World Cultural Heritage Site. The study suggested an integrated approach to understand tourists’ loyalty model and investigate the empirical evidence about the relationship among tourism products, destination image, risk perception, tourist experience, destination satisfaction and tourists’ loyalty. This study also mentions important questions concerning how tourism products, destination image, tourist experience, risk perception, and tourists’ satisfaction affect tourists’ loyalty. Smart PLS3 is used to estimate and test the relationships in the research model. Mediation analysis and importance performance matrix analysis are also used to consider clearly the relationship between the constructs of research model. The study’s results indicate that tourism products, destination image, tourism experience, risk perception, and satisfaction are antecedents of international tourists’ loyalty in Hoi An World Cultural Heritage Site. And in them, tourism products affect significantly positively to destination imagine and satisfaction, beside destination image and satisfaction hold the role of mediator in this relationship. Implementing IPMA to identify the predecessors that have relatively high importance for loyalty but also a relatively low performance. The results pointed out that the constructs as satisfaction, tourism product, risk perception and image have a high importance for the tourist loyalty. The study added the antecedent of tourism products and risk perception to the model and could enrich the literature, pointing to be possibility of a destination loyalty model that can be applied to various contexts, especially after COVID- 19 pandemic. The study also discussed theoretical and managerial implications for marketing tourism

AMRViz enables seamless genomics analysis and visualization of antimicrobial resistance

We have developed AMRViz, a toolkit for analyzing, visualizing, and managing bacterial genomics samples. The toolkit is bundled with the current best practice analysis pipeline allowing researchers to perform comprehensive analysis of a collection of samples directly from raw sequencing data with a single command line. The analysis results in a report showing the genome structure, genome annotations, antibiotic resistance and virulence profile for each sample. The pan-genome of all samples of the collection is analyzed to identify core- and accessory-genes. Phylogenies of the whole genome as well as all gene clusters are also generated. The toolkit provides a web-based visualization dashboard allowing researchers to interactively examine various aspects of the analysis results. Availability: AMRViz is implemented in Python and NodeJS, and is publicly available under open source MIT license at https://github.com/amromics/amrviz

PRELIMINARY STUDY OF THE ANTIOXIDANT PROPERTIES OF OPHIOCORDYCEPS SOBOLIFERA

The aim of study was to determine preliminary phytochemical analysis and the antioxidant potential of Ophiocordyceps sobolifera. The antioxidant activity of Ophiocordyceps sobolifera was evaluated using 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging and total antioxidant activity methods. Phytochemical analyses revealed the presence of steroids, triterpenoids, alkaloids, phenolics, flavoinods, protein, carbohydarte and saponins. The antioxidant activity of the ethanol extracts and water extracts showed high antioxidant activity with the lowest half maximal inhibitory concentration (IC50) values to 0.70 from 0.95mg/mL, realtively. Total antioxidant capacity of the O. sobolifera showed contained from 5.52 ± 0.14 to 12,71 ± 0.23 mg GA/g or from 3.55 ± 0.15 to 7.87 ± .05 μmol AS/g. These data suggest that O. sobolifera is a natural source of antioxidants

Applying DDPG Algorithm to Swing-Up and Balance Control for a Double Inverted Pendulum on a Cart

In this study, we apply the Deep Deterministic Policy Gradient (DDPG) algorithm in reinforcement learning to control a double inverted pendulum on a cart (DIPC)- a high order single input-multi output (SIMO) system . The simulation results demonstrate DDPG’s stability and effectiveness in achieving swing-up and balance, showing its potential for tackling challenging control tasks in robotics

In vitro antioxidant activity and bioactive compounds from Calocybe indica

Nowadays, the use of mushrooms in medicine is ubiquitous and has achieved particular success. The antioxidants in mushrooms can deactivate free radicals. This study assesses the antioxidant potential of mushroom Calocybe indica with the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical and 2,2′-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) radical scavenging methods and the total antioxidant capacity. The mushroom’s ethanol extract exhibits acceptable activity with a low IC50 value (240.11 μg/mL), approximately 2.9 times lower than that of the mushroom Ophiocordyceps sobolifera extract. The ABTS scavenging rate of the extract is around 60% at 500 µg/mL, and the total antioxidant capacity is equivalent to 64.94 ± 1.03 mg of GA/g or 77.42 ± 0.42 μmol of AS/g.  The total phenolics, flavonoids, polysaccharides, and triterpenoids are equivalent to 29.33 ± 0.16 mg of GAE/g, 17.84 ± 0.11 mg of QUE/g (5.04 ± 0.04%), and 4.96 ± 0.04 mg of oleanolic acid/g, respectively. Specifically, the total triterpenoid content has been reported for the first time. The mushroom can have potential biomedical applications

AMRomics: a scalable workflow to analyze large microbial genome collections

Whole genome analysis for microbial genomics is critical to studying and monitoring antimicrobial resistance strains. The exponential growth of microbial sequencing data necessitates a fast and scalable computational pipeline to generate the desired outputs in a timely and cost-effective manner. Recent methods have been implemented to integrate individual genomes into large collections of specific bacterial populations and are widely employed for systematic genomic surveillance. However, they do not scale well when the population expands and turnaround time remains the main issue for this type of analysis. Here, we introduce AMRomics, an optimized microbial genomics pipeline that can work efficiently with big datasets. We use different bacterial data collections to compare AMRomics against competitive tools and show that our pipeline can generate similar results of interest but with better performance. The software is open source and is publicly available at https://github.com/amromics/amromics under an MIT license

Polysaccharide extraction from Myxopyrum smilacifolium trunk and its antioxidant capacity

As a traditional medicinal plant in Vietnam, Myxopyrum smilacifolium has been used for a long history to treat cough, nervous disorders, numbness, rheumatism, and cephalalgia. Nevertheless, reports on the antioxidant activity and extraction of M. smilacifolium polysaccharides are still very rare. This study was designed to extract a high yield of polysaccharides from the M. smilacifolium trunk and characterize it. As a result, the maximum yield of the polysaccharides of 5.13 ± 0.05% was obtained with an extraction time of three hours, extraction temperature of 100 oC, the ratio of water to sample of 1:50 as extraction solution, extraction number of times 3, and the ratio of ethanol to extract volume 5:1 (v/v). Polysaccharides was characterized by Fourier transform infrared spectroscopy (FT-IR) and high-performance gel-permeation chromatography (HPGPC). The average molecular weight of extracted polysaccharides was around 3.78 × 105 Da. In vitro assays dan impressive antioxidant activities of the extracted polysaccharides, containing 0.2423 ± 0.0028 mg GA/g or 0.2142 ± 0.0007 μmol AS/g. The IC50 values of polysaccharides in the DPPH and ABTS methods were 0.89 mg/mL and 3.85 mg/mL, respectively.  These findings exhibited the potential for application or further research and development of polysaccharides from Myxopyrum smilacifolium