Search Results (26)

Background: Neisseria meningitidis (N. meningitidis) is a leading cause of acute meningitis and is classified into 13 serogroups, six of which are predominantly associated with invasive meningococcal disease. This study aimed to investigate the genotype, subgenotype, and antigenic profiles of N. meningitidis serogroup B strains isolated in Vietnam. Methods: Genotyping was performed on 106 N. meningitidis strains isolated from clinical samples from Vietnamese patients and nasopharyngeal swabs of healthy adolescents between 2019 and 2024. The genetic profiles, including the porA, porB, fetA, fHbp, abcZ, adk, aroE, fumC, gdh, pdhC, and pgm genes, were analyzed using Sanger sequencing and bioinformatic methods. Results: We found that 84.9% of the strains carried VR3 families 36 or 35-1, with VR1, VR2, and VR3 families 22-25, 14, and 36 being the most prevalent. Among the 106 serogroup B isolates, 20 variants of the porB allele 3 were identified, with porB 3-1212 being the most frequent (30.2%). Dominant PorB variable loops included L1.6, L4.5, L5.7, L6.6, and L7.13. fHbp variant group 2 was predominant (104/106 strains), and 12 FetA allele variants were identified, with F1-7 being the most common (47.2%). Three clonal complexes were identified, and clonal complex ST-32 was the most predominant. Fifty-five strains (51.9%) belonged to sequence types that have not yet been assigned to any clonal complexes, and 15 strains (14.1%) with allelic profiles were not assigned to STs. The 3-253 and 3-1212 alleles of porB, the F1-7 variant of FetA, the ST-44 and ST-1576 sequence types, and the ST-41/44 complex were observed more frequently in patients compared to asymptomatic carriers, suggesting their association with more virulence. Conclusions: This study showed a high genetic and antigenic diversity of N. meningitidis serogroup B isolates in Vietnam, with VR3 family 36 most common and porB 3-1212 as the predominant allele. fHbp variant group 2 and FetA allele F1-7 were most frequent. ST-32 was the dominant clonal complex, though many strains remained unassigned, highlighting the need for ongoing molecular surveillance. Full article

Campylobacter spp. are the causative agents of campylobacteriosis, a major foodborne illness globally, with millions of cases reported annually. These pathogens pose significant risks to both human and animal health. Conventional culture-based diagnostic methods are labor-intensive and time-consuming, underscoring the need for more efficient molecular detection strategies. This study employed a pangenomic analysis to identify novel gene-specific markers for pathogenic Campylobacter species and subspecies, laying the groundwork for their application in diverse diagnostic assays. A curated dataset of 105 high-quality genomes, representing 33 species and 9 subspecies, was analyzed using the Roary ILP Bacterial Annotation Pipeline. The results revealed substantial genomic diversity within the genus, with core gene counts varying across different nucleotide identity thresholds. Ribosomal genes such as rpsL, rpsJ, rpsS, rpmA, rpsK, rpsU, rpsG, rpmH, and rpsZ were consistently identified in the core genome, whereas accessory genes exhibited marked variability. This study uncovered novel and highly specific genetic markers for various Campylobacter species, including petB, clpX, and carB for C. coli; hypothetical proteins for C. jejuni and C. fetus; porA2 for C. lari; and mdtJ for C. upsaliensis. These markers demonstrated a specificity of at least 90% with minimal cross-reactivity with non-target organisms. The findings underscore the genomic heterogeneity within Campylobacter and provide essential genetic targets for the enhanced molecular detection of its pathogenic species, subspecies, and biovars. Full article

This study provides a bibliometric analysis of global scientific production on Conservation Agriculture (CA) and its relationship with climate change mitigation. Using data from the Scopus and Web of Science databases, the research encompassed 650 articles published between 1995 and 2022. The analysis revealed significant growth in the number of publications over the past three decades, driven by increasing global interest in sustainable agricultural practices. The findings highlight key themes, including no-tillage, soil organic carbon, and greenhouse gas emissions. Collaboration networks were mapped, identifying major contributors, such as the USA, Brazil, and China, alongside thematic clusters emphasizing carbon sequestration and soil management. Results indicate that CA research is increasingly focused on its potential to mitigate climate change, particularly through practices like no-tillage, vegetative cover, and crop rotation. While carbon sequestration has been central to CA research, recent studies have expanded to include nitrous oxide and methane emissions, indicating a broadening conceptual framework. This analysis underscores the importance of CA in addressing climate challenges and offers insights into emerging research areas, such as regional adaptations and the long-term effects of no-till systems. The findings aim to guide future research and policy development in sustainable agriculture and climate mitigation. Full article

Mitochondria is an important organelle for the oocyte-to-embryo transition in the early embryonic development period. The oocyte uses mitochondria functionally and its mitochondrial DNA (mtDNA) content as the main energy source in the embryo development at the preimplantation stage. The aim of this study is to compare mitophagic, apoptotic and humanin gene expressions from the culture medium fluid in which embryos are developed and monitored among normoresponder (NOR), polycystic ovary syndrome (PCOS), young and older patients with poor ovarian reserve (POR). The study groups consisted of infertile patients who applied to the Bahçeci Umut IVF Center as NOR (Control), PCOS, POR-Advanced (POR-A) and POR-Young (POR-Y). After the isolation of total RNA from the collected samples, MFN1, MFN2, PINK1, PARKIN, SMN1, SMN2, p53 and Humanin gene expressions were determined by Real Time-PCR. The average age of only the POR-A was determined to be higher than the NOR (p < 0.001). The MFN1, SMN2 (p < 0.05), Humanin and p53 gene expressions (p < 0.001) increased, while PINK1 gene expression decreased (p < 0.05), in the POR-Y compared to the NOR. A decrease in MFN2, PARKIN (p < 0.05) and PINK1 gene expressions was determined in the PCOS compared to the NOR (p < 0.001). Furthermore, a decrease was observed in MFN2, PINK1 (p < 0.001) and Humanin gene expressions compared to the NOR (p < 0.05). The current data are the first in the literature determining the apoptotic and mitophagic status of the oocyte. The current results prove that waste embryo culture fluid may provide a non-invasive profile for important cellular parameters such as mitochondrial dysfunction in female infertility. The evaluation of significant cellular parameters can be performed much earlier without any intervention into the embryo. Full article

Glioblastoma multiforme (GBM)is the most common and aggressive primary brain tumor. Although temozolomide (TMZ)-based radiochemotherapy improves overall GBM patients’ survival, it also increases the frequency of false positive post-treatment magnetic resonance imaging (MRI) assessments for tumor progression. Pseudo-progression (PsP) is a treatment-related reaction with an increased contrast-enhancing lesion size at the tumor site or resection margins miming tumor recurrence on MRI. The accurate and reliable prognostication of GBM progression is urgently needed in the clinical management of GBM patients. Clinical data analysis indicates that the patients with PsP had superior overall and progression-free survival rates. In this study, we aimed to develop a prognostic model to evaluate the tumor progression potential of GBM patients following standard therapies. We applied a dictionary learning scheme to obtain imaging features of GBM patients with PsP or true tumor progression (TTP) from the Wake dataset. Based on these radiographic features, we conducted a radiogenomics analysis to identify the significantly associated genes. These significantly associated genes were used as features to construct a 2YS (2-year survival rate) logistic regression model. GBM patients were classified into low- and high-survival risk groups based on the individual 2YS scores derived from this model. We tested our model using an independent The Cancer Genome Atlas Program (TCGA) dataset and found that 2YS scores were significantly associated with the patient’s overall survival. We used two cohorts of the TCGA data to train and test our model. Our results show that the 2YS scores-based classification results from the training and testing TCGA datasets were significantly associated with the overall survival of patients. We also analyzed the survival prediction ability of other clinical factors (gender, age, KPS (Karnofsky performance status), normal cell ratio) and found that these factors were unrelated or weakly correlated with patients’ survival. Overall, our studies have demonstrated the effectiveness and robustness of the 2YS model in predicting the clinical outcomes of GBM patients after standard therapies. Full article

In nature, the symbiotic relationship between plants and microorganisms is crucial for ecosystem balance and plant growth. This study investigates the impact of Epichloë endophytic fungi, which are exclusively present aboveground, on the rhizosphere microbial functions of the host Melica transsilvanica. Using metagenomic methods, we analyzed the differences in microbial functional groups and functional genes in the rhizosphere soil between symbiotic (EI) and non-symbiotic (EF) plants. The results reveal that the presence of Epichloë altered the community structure of carbon and nitrogen cycling-related microbial populations in the host’s rhizosphere, significantly increasing the abundance of the genes (porA, porG, IDH1) involved in the rTCA cycle of the carbon fixation pathway, as well as the abundance of nxrAB genes related to nitrification in the nitrogen-cycling pathway. Furthermore, the presence of Epichloë reduces the enrichment of virulence factors in the host rhizosphere microbiome, while significantly increasing the accumulation of resistance genes against heavy metals such as Zn, Sb, and Pb. This study provides new insights into the interactions among endophytic fungi, host plants, and rhizosphere microorganisms, and offers potential applications for utilizing endophytic fungi resources to improve plant growth and soil health. Full article

Water deficit is one of the factors that most influence plant growth and yield. Thus, this study aimed to evaluate the effect of silicon and salicylic acid application and water deficit on the growth and photosynthetic and osmoregulatory metabolism of Talisia esculenta Radlk. seedlings and their recovery potential after the resumption of irrigation. Six treatments were performed: irrigation, irrigation suspension, irrigation suspension + silicon at 0.5 g L⁻¹, irrigation suspension + silicon at 1.0 g L⁻¹, irrigation suspension + salicylic acid at 50 mg L⁻¹, and irrigation suspension + salicylic acid at 100 mg L⁻¹. The evaluations were carried out at the beginning of the experiment, at 10 and 15 days after irrigation suspension, when the seedlings showed a photosynthetic rate close to zero, and at recovery. The plants were subjected to water restriction for up to 15 days, then re-irrigated until the recovery point, which was monitored based on the photosynthetic rate. Silicon application attenuated the harmful effects of water deficit on gas exchange and initial fluorescence, promoted proline accumulation in the leaf and root, and provided higher seedling quality. Salicylic acid application contributed to the maintenance of the relative water content of leaves during the water deficit period. Silicon and salicylic acid applications can attenuate the harmful effects of water stress, with silicon being the most effective agent in maintaining its growth and metabolism. Full article

Herein, we report results of the studies relating to the development of an impedimetric, magnetic bead-assisted supersandwich DNA hybridization assay for ultrasensitive detection of Neisseria gonorrhoeae, the causative agent of a sexually transmitted infection (STI), gonorrhea. First, a conductive ink was formulated by homogenously dispersing carboxylated multiwalled carbon nanotubes (cMWCNTs) in a stable emulsion of terpineol and an aqueous suspension of carboxymethyl cellulose (CMC). The ink, labeled C5, was coated onto paper substrates to fabricate C5@paper conductive electrodes. Thereafter, a magnetic bead (MB)-assisted supersandwich DNA hybridization assay was optimized against the porA pseudogene of N. gonorrhoeae. For this purpose, a pair of specific 5′ aminated capture probes (SCP) and supersandwich detector probes (SDP) was designed, which allowed the enrichment of target gonorrheal DNA sequence from a milieu of substances. The SD probe was designed such that instead of 1:1 binding, it allowed the binding of more than one T strand, leading to a ‘ladder-like’ DNA supersandwich structure. The MB-assisted supersandwich assay was integrated into the C5@paper electrodes for electrochemical analysis. The C5@paper electrodes were found to be highly conductive by a four-probe conductivity method (maximum conductivity of 10.1 S·cm⁻¹). Further, the biosensing assay displayed a wide linear range of 100 aM-100 nM (10⁹ orders of magnitude) with an excellent sensitivity of 22.6 kΩ·(log[concentration])⁻¹. The clinical applicability of the biosensing assay was assessed by detecting genomic DNA extracted from N. gonorrhoeae in the presence of DNA from different non-gonorrheal bacterial species. In conclusion, this study demonstrates a highly sensitive, cost-effective, and label-free paper-based device for STI diagnostics. The ink formulation prepared for the study was found to be highly thixotropic, which indicates that the paper electrodes can be screen-printed in a reproducible and scalable manner. Full article

Parkinson’s disease (PD) is characterized by dopaminergic neurodegeneration and an abnormal accumulation of α-synuclein aggregates. A number of genetic factors have been shown to increase the risk of PD. Exploring the underlying molecular mechanisms that mediate PD’s transcriptomic diversity can help us understand neurodegenerative pathogenesis. In this study, we identified 9897 A-to-I RNA editing events associated with 6286 genes across 372 PD patients. Of them, 72 RNA editing events altered miRNA binding sites and this may directly affect miRNA regulations of their host genes. However, RNA editing effects on the miRNA regulation of genes are more complex. They can (1) abolish existing miRNA binding sites, which allows miRNAs to regulate other genes; (2) create new miRNA binding sites that may sequester miRNAs from regulating other genes; or (3) occur in the miRNA seed regions and change their targets. The first two processes are also referred to as miRNA competitive binding. In our study, we found 8 RNA editing events that may alter the expression of 1146 other genes via miRNA competition. We also found one RNA editing event that modified a miRNA seed region, which was predicted to disturb the regulation of four genes. Considering the PD-related functions of the affected genes, 25 A-to-I RNA editing biomarkers for PD are proposed, including the 3 editing events in the EIF2AK2, APOL6, and miR-4477b seed regions. These biomarkers may alter the miRNA regulation of 133 PD-related genes. All these analyses reveal the potential mechanisms and regulations of RNA editing in PD pathogenesis. Full article

The photoreceptors of red light (phytochromes) and blue light (cryptochromes) impact plant growth and metabolism. However, their action has been barely studied, especially in coniferous plants. Therefore, the influence of blue (maximum 450 nm), red (maximum 660 nm), white light (maxima 450 nm + 575 nm), far-red light (maximum 730 nm), white fluorescent light and dark on seed germination, growth, chlorophyll and carotenoid contents, as well as the transcript levels of genes involved in reception, photosynthesis, light and hormonal signaling of Scots pine plantlets, was investigated. The highest values of dry weight, root length and photosynthetic pigment contents were characteristic of 9-day-old plantlets grown under red light, whereas in the dark plantlet length, seed vigor, seed germination, dry weight and pigment contents were decreased. Under blue and white lights, the main studied morphological parameters were decreased or close to red light. The cotyledons were undeveloped under dark conditions, likely due to the reduced content of photosynthetic pigments, which agrees with the low transcript levels of genes encoding protochlorophyllide oxidoreductase (PORA) and phytoene synthase (PSY). The transcript levels of a number of genes involved in phytohormone biosynthesis and signaling, such as GA3ox, RRa, KAO and JazA, were enhanced under red light, unlike under dark conditions. We suggest that the observed phenomena of red light are the most important for the germination of the plantlets and may be based on earlier and enhanced expression of auxin, cytokinin, gibberellin and jasmonate signaling genes activated by corresponding photoreceptors. The obtained results may help to improve reforestation technology; however, this problem needs further study. Full article

Low-GI biscuits are commonly produced using whole-grain flour, bran, or soluble dietary fibers, giving an undesirable texture. New low-GI biscuits containing dietary fibers and with improved palatability were formulated by substituting 60% of wheat flour (WF) with a native starch (ST) and 15% of WF with a resistant dextrin (RD), a source of dietary fibers. The botanical source of ST was common buckwheat (Fagopyrum esculentum Moench). Biscuits were also made with a single substitution by ST or by RD at the same level for comparison. The firmness of the biscuits was increased with the single substitution by RD due to its small average molecular size and high hygroscopicity, while it was decreased with the single substitution by ST. The double substitution by ST and RD not only produced the texture with the lowest firmness and brittleness, but also led to the lowest in vitro starch digestion rate and total starch digestibility. The human trial confirmed that the biscuits with the double substitution had a low GI of 47. The results indicated the additive or synergistic effects of ST and RD on the properties of the biscuits, demonstrating that low-GI biscuits can be produced with a substantial dietary fiber content without jeopardizing their palatability. Full article

This paper proposes a new deterministic branch prediction unit to achieve a uniformly timed instruction set architecture (ISA). The deterministic ISA is achieved by utilizing two address buses in conjunction with dual-port block RAMs that are common in commercial FPGAs. The goal is to remove mandatory branch and load delays to achieve a uniform one clock cycle per every instruction. To demonstrate the concept, the proposed architecture is applied to the Xilinx PicoBlaze firm core. The result is a new soft core named DAP-Zipi8 that reduces the clock per instruction (CPI) metric of PicoBlaze from two to one at the expense of extra logic and a longer critical path. The increased critical path reduces maximum achievable clock speed from 357.509 MHz to 224.022 MHz. Merging the gain in CPI with the loss in maximum clock frequency still improves overall processor performance by 18.28–19.49%. The high-performance deterministic DAP-Zipi8 is a viable choice for hard RTES applications. Full article

Insect-vectored plant viruses pose a serious threat to sustainable production of economically important crops worldwide. This demands a continuous search for environmentally-friendly, sustainable and efficient approaches based on biological agents to address the mounting challenges of viral disease management. To date, the efficacy of actinomycetes bacteria against DNA plant viruses remains unknown. Here, through comparative analyses, we demonstrate that the RFS-23 strain of Streptomyces cellulase possesses protective activity as it positively regulated the plant growth and development. and diminished the severity, of disease symptoms, together with reduced accumulation of Tomato yellow leaf curl virus (TYLCV) DNA. The RFS-23 strain maintained relative chlorophyll contents by promoting the expression of genes (CLH1, HEMA1 and PORA) associated with chlorophyll biogenesis. As compared to another strain, CTF-20, the RSF-23 induced a significantly higher expression of plant defense-related genes (NbCIS and NbNCED) associated with biogenesis and accumulation of salicylic acid and abscisic acid. Additionally, the activity of antioxidant enzymes (SOD, CAT, POD and MDA) was significantly enhanced by RSF-23 treatment, despite the presence of viral infection. These findings suggest that RSF-23 is a novel biocontrol agent with protective activity, and it could be a potential candidate for the management of plant viral infections. Full article

Phenylacetylglutamine (PAGln), a gut microbiota (GM)-derived metabolite, is associated with cardiovascular disease. Studies have shown that disordered GM participated in the progression of atrial fibrillation (AF), but the relationship between PAGln and AF is unclear. This study investigated the characteristics of PAGln in AF patients and its impact on atrial myocytes. Based on our previous metagenomic data, the relative abundance of porA, a critical bacterial enzyme for PAGln synthesis, exhibited an increased tendency in AF. In an independent cohort consisting of 42 controls without AF and 92 AF patients, plasma PAGln levels were higher in AF patients than in controls (p < 0.001) by immunoassay. Notably, PAGln exerted a predictive potential of AF with an AUC of 0.774 (p < 0.001), and a predictive model constructed based on the PAGln and Taiwan AF score further improved the predictive potential. Furthermore, a positive correlation was determined between PAGln and LA diameter. Subsequently, the effect of PAGln intervention was examined on HL-1 cells in vitro, revealing that PAGln increased apoptosis, reactive oxygen species (ROS) production, CaMKII and RyR2 activation and decreased cell viability. In conclusion, increased PAGln was associated with AF, and PAGln might contribute to the AF pathogenesis by promoting oxidative stress and apoptosis in atrial myocytes. Full article

Maintenance activities to replace, repair, and revamp equipment in the industrial plant sector are gradually needed for sustainability during the plant’s life cycle. In order to carry out these revamping activities, the plant owners exchange many purchase orders (POs) with equipment suppliers, including technical and specification documents and commercial procurement content. As POs are written in various formats with large volumes and complexities, it is often time-consuming for the owner’s engineer to review them and it may lead to errors and omissions. This study proposed the purchase order recognition and analysis system (PORAS), which automatically detects and compares risk clauses between plant owners’ and suppliers’ POs by utilizing artificial intelligence (AI). The PORAS is a comprehensive framework consisting of two independent modules and four model components that accurately reflect on the added value of the PORAS. The table recognition and comparison (TRC) module is utilized for risk clauses in POs written in tables with its two components, the table comparison (TRC-C) and table recognition (TRC-R) models. The critical terms in general conditions (CTGC) module analyzes the patterns of risk clauses in general texts, then extracts them with a rule-based algorithm and compares them through entity matching. In the TRC-C model using machine learning (Ditto model), a few errors occurred due to insufficient training data, resulting in an accuracy of 87.8%, whereas in the TRC-R model, a rule-based algorithm, errors occurred in only some exceptional cases; thus, its F1 score was evaluated to be 96.9%. The CTGC module’s F2 score for automatic extraction performance was evaluated as 79.1% due to some data’s bias. Overall, the validation study shows that while a human review of the risk clauses in a PO manually took hours, it took only an average of 10 min with the PORAS. Therefore, this time saving can significantly reduce the owner engineer’s PO workload. In essence, this study contributes to achieving sustainable engineering processes through the intelligence and automation of document and risk management in the plant industry. Full article