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Comparative Evaluation of Open-Source Bioinformatics Pipelines for Full-Length Viral Genome Assembly.
Viruses
November 2024
Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary.
The increasingly widespread application of next-generation sequencing (NGS) in clinical diagnostics and epidemiological research has generated a demand for robust, fast, automated, and user-friendly bioinformatics workflows. To guide the choice of tools for the assembly of full-length viral genomes from NGS datasets, we assessed the performance and applicability of four open-source bioinformatics pipelines (shiver-for which we created a user-friendly Dockerized version, referred to as dshiver; SmaltAlign; viral-ngs; and V-pipe) using both simulated and real-world HIV-1 paired-end short-read datasets and default settings. All four pipelines produced consensus genome assemblies with high quality metrics (genome fraction recovery, mismatch and indel rates, variant calling F1 scores) when the reference sequence used for assembly had high similarity to the analyzed sample.
View Article and Find Full Text PDFComprehensive In Vitro Evaluation of Antibacterial, Antioxidant, and Computational Insights into (L.) B. L. Burtt from Hail Mountains, Saudi Arabia.
Plants (Basel)
December 2024
Department of Biology, College of Science, Qassim University, Qassim 51452, Saudi Arabia.
The arid mountainous region of Hail in Saudi Arabia has a variety of desert vegetation, some of which are conventionally used in Bedouin traditional medicine. These plants need scientific examination. This research seeks to examine using a thorough multi-analytical methodology that includes antibacterial and antioxidant assessments as well as computational modeling.
View Article and Find Full Text PDFMicronutrient Status in Patients with Severe Obesity Before and After Laparoscopic Sleeve Gastrectomy.
Nutrients
December 2024
Department of Pharmaceutical Botany, Faculty of Pharmacy, "Iuliu Hatieganu" University of Medicine and Pharmacy, 400337 Cluj-Napoca, Romania.
Micronutrient deficiencies (MNDs) are commonly reported after bariatric and metabolic surgery, including laparoscopic sleeve gastrectomy (LSG). Nevertheless, the micronutrient status changes over time and the influence of sex or initial body mass index (BMI) on these changes are less explored. This study aims to investigate the changes in micronutrient levels at 6 and 12 months after LSG and the potential influence of sex or baseline BMI (≥40 kg/m) on these changes in patients submitted to LSG.
View Article and Find Full Text PDFAnti-Epileptic Activity of Mitocurcumin in a Zebrafish-Pentylenetetrazole (PTZ) Epilepsy Model.
Pharmaceuticals (Basel)
November 2024
Discipline of Pharmacology, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy Iasi, 16 Universitatii Street, 700115 Iasi, Romania.
: Ongoing challenges in epilepsy therapy warrant research on alternative treatments that offer improved efficacy and reduced side effects. Designed to enhance mitochondrial targeting and increase bioavailability, mitocurcumin (MitoCur) was evaluated for the first time as an antiepileptic agent, with curcumin (Cur) and sodium valproate (VPA), a standard antiepileptic drug, included for comparison. This study investigated the effects on seizure onset, severity, and progression in a zebrafish model of pentylenetetrazole (PTZ)-induced seizures and measured the concentrations of the compounds in brain tissue.
View Article and Find Full Text PDFCorrection: Qiu et al. Genistein Modified with 8-Prenyl Group Suppresses Osteoclast Activity Directly via Its Prototype but Not Metabolite by Gut Microbiota. 2022, , 7811.
Molecules
December 2024
State Key Laboratory of Chinese Medicine and Molecular Pharmacology (Incubation), Shenzhen Research Institute of the Hong Kong Polytechnic University, Shenzhen 518057, China.
In the original publication [...
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