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Sanger validation of WGS variants
Abstract With the development of next-generation sequencing (NGS) technologies it became possible to simultaneously analyze millions of variants. Despite the quality improvement, it is generally still required to confirm the variants before reporting. However, in recent years the dominant idea is that one could define the quality thresholds for “high quality” variants which do not require orthogonal validation. Despite that, no works to date report the concordance between variants from whole genome sequencing and their gold-standard Sanger validation. In this study we analyzed the concordance for 1756 WGS variants in order to establish the appropriate thresholds for high-quality variants filtering. Resulting thresholds allowed us to drastically reduce the number of variants which require validation, to 4.8% and 1.2% of the initial set for caller-agnostic (DP, AF) and caller-dependent (QUAL) thresholds, respectively.
Altered mitochondrial unfolded protein response and FGF21 secretion in MASLD progression and the effect of exercise intervention
Emergence of opposing arrows of time in open quantum systems
Abstract Deriving an arrow of time from time-reversal symmetric microscopic dynamics is a fundamental open problem in many areas of physics, ranging from cosmology, to particle physics, to thermodynamics and statistical mechanics. Here we focus on the derivation of the arrow of time in open quantum systems and study precisely how time-reversal symmetry is broken. This derivation involves the Markov approximation applied to a system interacting with an infinite heat bath. We find that the Markov approximation does not imply a violation of time-reversal symmetry. Our results show instead that the time-reversal symmetry is maintained in the derived equations of motion. This imposes a time-symmetric formulation of quantum Brownian motion, Lindblad and Pauli master equations, which hence describe thermalisation that may occur into two opposing time directions. As a consequence, we argue that these dynamics are better described by a time-symmetric definition of Markovianity. Our results may reflect on the formulations of the arrow of time in thermodynamics, cosmology, and quantum mechanics.
Impact of polyvinyl chloride nano-plastics on the biochemical status of Oreochromis niloticus under a predicted global warming scenario
Abstract Plastic pollution and global warming are widespread issues that lead to several impacts on aquatic organisms. Despite harmful studies on both subjects, there are few studies on how temperature increases plastics’ adverse effects on aquatic animals, mainly freshwater species. So, this study aims to clarify the potential impact of temperature increases on the toxicological properties of polyvinyl chloride nano-plastics (PVC-NPs) in Nile tilapia (Oreochromis niloticus) by measuring biochemical and oxidative biomarkers. The fish groups were subjected to three distinct temperatures (30, 32, and 34 °C) and subsequently separated into two groups: 0 and 10 mg/L of PVC-NPs, as it is expected that these temperatures may modify their chemical properties, which can influence their absorption and toxicity in fish. After 4 days, the biochemical response of fish exposed to PVC-NPs and elevated temperatures showed a significant increase in the levels of plasma total proteins, albumin, globulin, aspartate aminotransferase (AST), alanine aminotransferase (ALT), alkaline phosphatase (ALP), creatinine, and uric acid. Additionally, the level of oxidative stress biomarkers in the liver, gills, and brain was found to have a significant increase in malondialdehyde (MDA) concentration and a decrease in glutathione reduced (GSH) concentration and catalase (CAT) activity in all studied groups. Finally, the current findings revealed a synergistic cytotoxic effect of PVC-NPs and temperatures on the metabolic and oxidative stress indices of O. niloticus.
Factors contributing to helminth prevalence after repeated mass administration of medicines in Anambra State, Nigeria
Abstract Over the past decade, Mass Administration of Medicines (MAM) has been a key strategy for controlling schistosomiasis and soil-transmitted helminthiasis (STHs) in Anambra State, Nigeria. This longitudinal study, conducted from 2017 to 2019, evaluated the impact of interventions for controlling schistosomiasis (SCH) and STHs in recipient communities. A total of 1,046 pupils aged 5 to 16 years were enrolled, with Kato-Katz and urine filtration methods used for faecal and urine sample analysis. A structured questionnaire was administered to 243 people to assess the contextual factors. At baseline, prevalence was 8% (82/1046), with A. lumbricoides (7.0%), T. trichiura (1.0%), Hookworm (0.1%), and S. haematobium (0.5%) observed. Co-infection was 1%. At follow-up, prevalence decreased to 6% (65/1046), with A. lumbricoides (2.0%), T. trichiura (2.2%), and S. haematobium (2%) observed, and co-infection was 0.2%. Infection levels varied by location ( p > 0.05), with socio-economic status and inadequate WASH (Water, Sanitation, and Hygiene) infrastructure contributing to transmission risk. Most respondents (87%) earned less than $50 per month, and 39% practiced open defecation. The persistence of open defecation highlights critical gaps in WASH that undermine sustainable Neglected Tropical Diseases (NTD) control. Addressing cultural and economic challenges, alongside improving WASH infrastructure, is essential to sustain MAM’s impact.
Fish active packaging with ZnO/Fe-MMT nanoparticles
Comprehensive computational analysis of differentially expressed miRNAs and their influence on transcriptomic signatures in prostate cancer
The impact of carbon emissions trading on green total factor productivity based on evidence from a quasi-natural experiment
Impact of choline choride and sugar natural deep eutectic solvents on structure and functionality of treebean (Parkia timoriana) seed protein
The efficacy of non-depolarizing muscle relaxant as adjuvants to local anesthesia in peribulbar block during cataract surgery
Abstract Peribulbar anesthesia is mainly used for cataract surgery. Many studies had used atracurium and rocuronium as an additive to the local anesthetic (LA) drugs in eye surgery. The aim of this study is to evaluate the efficacy of adding atracurium versus rocuronium to a local anesthetic mixture, in providing an early onset of orbital akinesia and corneal anesthesia during cataract surgery. Ninety-three patients met the inclusion criteria and gave a written informed consent to participate. Patients were randomly allocated in three study groups (31 patients in each group). Group I received either 3 mL of a lidocaine2%(mixed by hyaluronidase 50 IU/ml) and 3 ml bupivacaine mixture, plus 0.5 mL rocuronium (5 mg) total volume 6.5 ml. Group II 3 mL of a lidocaine2%(mixed by hyaluronidase 50 IU/ml) and 3 ml bupivacaine mixture plus 0.5 mL (5 mg) atracurium total volume 6.5 ml. Group III or3 mL of a lidocaine2%(mixed by hyaluronidase 50 IU/ml) and − 3 ml bupivacaine mixture, plus 0.5 mL saline total volume 6.5 ml. The onset time of orbital akinesia was significantly lower in the rocuronium group and the atracurium group compared to the control group. Akinesia score was (0.90 ± 0.30) and (0.19 ± 0.40) in rocuronium group at 4 min and 6 min respectively which result in highly significant difference than atracurium and control groups. The use of rocuronium and atracurium will result in rapid orbital akinesia and rapid orbicularis muscle akinesia.
Publisher Correction: Starvation-induced metabolic rewiring affects mTORC1 composition in vivo
Thermostable terahertz metasurface enabled by graphene assembly film for plasmon-induced transparency
Evaluating the effects of chlorhexidine and vitamin c mouthwash on oral health in non-surgical periodontal therapy: a randomized controlled clinical trial
Understanding and promoting equitable post-discharge care in firearm injury survivors: a retrospective chart review
A volumetric study of the choroid plexus in neuropsychiatric systemic lupus erythematosus
Ecofriendly remediation of cadmium, lead, and zinc using dead cells of Microcystis aeruginosa
Abstract The utilization of cyanobacteria toxin-producing blooms for metal ions adsorption has garnered significant attention over the last decade. This study investigates the efficacy of dead cells from Microcystis aeruginosa blooms, collected from agricultural drainage water reservoir, in removing of cadmium, lead, and zinc ions from aqueous solutions, and simultaneously addressing the mitigation of toxin-producing M. aeruginosa bloom. Some physical characterization of the dead biomass was performed, including scanning electron microscope (SEM) which revealed that, the cells form a dense, amorphous cluster, energy-dispersive X-ray (EDX) spectroscopy confirmed that carbon, oxygen, and nitrogen are the predominant elements in the biomass, Fourier transformation infrared (FTIR) spectroscopy identified several active function groups, including hydroxyl, aliphatic C–H amide I and amide II bands, carboxylate and carbonyl (C=O). Key factors influencing the adsorption process were examined. Under optimal conditions—pH 6, a biosorbent dose of 0.3 g, contact time of 90 min, primary metal level of 100 mg/L and temperature of 35 °C (313K)—a maximum removal efficiency exceeding 90% was achieved. Isothermal analysis revealed that the adsorption of Cd(II), Pb(II), and Zn(II) followed the Langmuir isotherm model (R2 = 0.96, q max > 67 mg/g). Kinetic studies indicated that the pseudo-second-order model best described the adsorption process (R2 > 0.94 and q e > 81.3 mg/g.), suggesting a dominant chemisorption mechanism. Thermodynamic analysis indicated that the adsorption process is spontaneous and endothermic. The findings highlight the potential of M. aeruginosa dead cells as a low-cost, sustainable biosorbent for the removal of heavy metal in wastewater treatment applications.
scATAC-seq generates more accurate and complete regulatory maps than bulk ATAC-seq
Abstract Bulk ATAC-seq assays have been used to map and profile the chromatin accessibility of regulatory elements such as enhancers, promoters, and insulators. This has provided great insight into the regulation of gene expression in many cell types in a variety of organisms. To date, ATAC-seq has most often been used to provide an average evaluation of chromatin accessibility in populations of cells. The development of a single cell approach (scATAC-seq) assay enables researchers to evaluate chromatin accessibility in individual cells and identify sub-groups in mixed populations of cells. To investigate the full potential of single-cell epigenomic data, we have comprehensively compared the information derived from bulk ATAC-seq and scATAC-seq in populations of cells. We found that the chromatin architecture signal is the same using bulk ATAC-seq and scATAC-seq to analyse aliquots of the same cell population. However, scATAC-seq provides substantially higher data quality compared to bulk ATAC-seq improving the sensitivity to detect relatively weak, but functionally important ATAC-seq signals. Furthermore, we found that scATAC-seq identified differences in what was previously assumed to be a homogenous population of cells. Finally, we determined the number of cells required to generate aggregated open chromatin profiles from single cells and to identify biologically meaningful clusters after pseudo-bulking of data. This study illustrates the added value of using scATAC-seq rather than bulk ATAC-seq in evaluating both homogeneous and heterogeneous populations of cells. This paper provides a comprehensive guide on the benefits of using scATAC-seq data to study gene regulation.