Search Results (1,576)

With the continuous development of industrial automation, diesel engines play an increasingly important role in various types of construction machinery and power generation equipment. Improving the dynamic and static performance of the speed control system of single-cylinder diesel engines can not only significantly improve the efficiency of the equipment, but also effectively reduce energy consumption and emissions. Particle swarm optimization (PSO) fuzzy PID control algorithms have been widely used in many complex engineering problems due to their powerful global optimization capability and excellent adaptability. Currently, PSO-based fuzzy PID control research mainly integrates hybrid algorithmic strategies to avoid the local optimum problem, and lacks optimization of the dynamic noise suppression of the input error and the rate of change of the error. This makes the algorithm susceptible to the coupling of the system uncertainty and measurement disturbances during the parameter optimization process, leading to performance degradation. For this reason, this study proposes a new framework based on the synergistic optimization of the untraceable Kalman filter (UKF) and PSO fuzzy PID control for the speed control system of a single-cylinder diesel engine. A PSO-optimized fuzzy PID controller is designed by obtaining accurate speed estimation data using the UKF. The PSO is capable of quickly adjusting the fuzzy PID parameters so as to effectively alleviate the nonlinearity and uncertainty problems during the operation of diesel engines. By establishing a Matlab/Simulink simulation model, the diesel engine speed step response experiments (i.e., startup experiments) and load mutation experiments were carried out, and the measurement noise and process noise were imposed. The simulation results show that the optimized diesel engine speed control system is able to reduce the overshoot by 76%, shorten the regulation time by 58%, and improve the noise reduction by 25% compared with the conventional PID control. Compared with the PSO fuzzy PID control algorithm without UKF noise reduction, the optimized scheme reduces the overshoot by 20%, shortens the regulation time by 48%, and improves the noise reduction effect by 23%. The results show that the PSO fuzzy PID control method with integrated UKF has superior control performance in terms of system stability and accuracy. The algorithm significantly improves the responsiveness and stability of diesel engine speed, achieves better control effect in the optimization of diesel engine speed control, and provides a useful reference for the optimization of other diesel engine control systems. In addition, this study establishes the GT-POWER model of a 168 F single-cylinder diesel engine, and compares the cylinder pressure and fuel consumption under four operating conditions through bench tests to ensure the physical reasonableness of the kinetic input parameters and avoid algorithmic optimization on the distorted front-end model. Full article

Acute Hemorrhagic Conjunctivitis (AHC) is primarily caused by viral infections, with Coxsackievirus A-24v (CV-A24v) being a significant culprit. Enteroviruses, including CV-A24v, are responsible for global AHC outbreaks. Over time, CV-A24v has evolved, and genotype IV (GIV) has become the dominant strain. This study focused on examining the genetic features and evolutionary trends of CV-A24v responsible for the recent AHC outbreak of 2023 in India. Researchers isolated viral strains from ocular swabs and confirmed the presence of CV-A24v using reverse transcriptase quantitative PCR (RT-qPCR) and whole-genome sequencing. Genomic comparisons between isolates of 2023 and those from a previous outbreak in 2009 were conducted. Phylogenetic analysis revealed that the 2023 isolates formed a distinct cluster within GIV-5 and were related to recent strains from China and Pakistan. The older Indian isolates from 2009 grouped with GIV-3. New subclades, GIV-6 and GIV-7, were also identified in this study, indicating the diversification of CV-A24. Molecular clock and phylogeographic analysis traced the virus’s circulation back to the 1960s, with the common ancestor likely to have originated in Singapore in 1968. The 2023 Indian strains probably originated from Thailand around 2014, with subsequent spread to China and Pakistan. This study concluded that the 2023 outbreak was caused by a genetically distinct CV-A24v strain with nine mutations, underlining the virus’s ongoing evolution and adaptations and offering valuable insights for future outbreak control. Full article

The DIR (Dirigent) gene family plays a multifaceted role in plant growth, development, and stress responses, making it one of the key gene families for plant adaptation to environmental changes. However, research on ZmDIRs in maize remains limited. In this study, we identified a member of the maize DIR gene family, ZmDIR5, whose promoter region contains numerous elements associated with responses to abiotic stresses. ZmDIR5 is upregulated in response to waterlogging, salt, and drought stresses, and its protein is localized in the endoplasmic reticulum. Subsequent studies revealed that ZmDIR5-EMS (ethyl methane sulfonate) mutant lines exhibited reduced growth compared to WT (wild-type) plants under waterlogging, salt, and drought stress conditions. The mutant lines also demonstrated a relatively higher accumulation of malondialdehyde and reactive oxygen species, lower synthesis of proline and total lignans, and decreased antioxidant enzyme activity under these stress conditions. Additionally, the mutant lines displayed impaired sodium and potassium ion transport capabilities, reduced synthesis of abscisic acid and zeatin, and decreased expression of related genes. The mutation of ZmDIR5 also inhibited the phenylpropanoid biosynthesis pathway in maize. These results indicate that ZmDIR5 serves as a positive regulator of maize tolerance to waterlogging, salt, and drought stresses. Full article

Intelligent optimization algorithms are crucial for solving complex engineering problems. The Parrot Optimization (PO) algorithm shows potential but has issues like local-optimum trapping and slow convergence. This study presents the Chaotic–Gaussian–Barycenter Parrot Optimization (CGBPO), a modified PO algorithm. CGBPO addresses these problems in three ways: using chaotic logistic mapping for random initialization to boost population diversity, applying Gaussian mutation to updated individual positions to avoid premature local-optimum convergence, and integrating a barycenter opposition-based learning strategy during iterations to expand the search space. Evaluated on the CEC2017 and CEC2022 benchmark suites against seven other algorithms, CGBPO outperforms them in convergence speed, solution accuracy, and stability. When applied to two practical engineering problems, CGBPO demonstrates superior adaptability and robustness. In an indoor visible light positioning simulation, CGBPO’s estimated positions are closer to the actual ones compared to PO, with the best coverage and smallest average error. Full article

The present paper addresses topics from various fields of biology. Its purpose is to enlarge the understanding of the usage of bioinformatics tools in the phylogenetic analysis of RNA viruses. The paper highlights the benefits of using information technology in virology, bringing the scientific community closer to unraveling the mysteries of RNA virus evolution and their adaptation to different niches and hosts and facilitating the understanding of their rapid mutation processes. Phylogenetic analysis of genetic sequences allows the exploration of the causes of these genetic changes in viruses and categorizes them into taxonomic groups. This paper is a systematic review of the most important scientific articles on the phylogenetic analysis of RNA viruses using bioinformatics. The studies included in the review were selected based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA 2020) guidelines and discuss methods for analyzing genetic and protein sequences (including codon sequences) and describe phylogenetic analyses and the bioinformatics tools used (such as VConTACT, RAxML, etc.). This review emphasizes the importance of further development in the fields of bioinformatics and virology, particularly with respect to RNA viruses, in order to mitigate the risk of a future pandemic. It also aims to provide a detailed understanding of the mutation and evolution mechanisms of these entities, which will help in efforts to limit viral virulence, for example. This article did not receive any funding for its creation and has not been registered in any database. Full article

The plateau pika (pl-pika), a resilient mammal of the Qinghai-Tibet Plateau, exhibits remarkable adaptations to extreme conditions. This study delves into mutations within the Endothelial PAS Domain Protein 1 (EPAS1) gene, crucial for high-altitude survival. Surprisingly, a novel 6-bp insertion/deletion (indel) mutation in EPAS1’s Intron 13, along with an additional repeat unit downstream, was discovered during PCR amplification. Genetic analysis across altitude gradients revealed a correlation between this indel’s frequency and altitude, hinting at its role in altitude adaptation. Fluorescence enzyme assays unveiled enhancer activity within Intron 13, where the deletion of repeat units led to increased activity, indicating potential transcription factor binding. Notably, GCM1 emerged as a candidate transcription factor binding to the indel site, suggesting its involvement in EPAS1 regulation. These findings enrich our comprehension of high-altitude adaptation in plateau pikas, shedding light on the intricate interplay between genetic mutations, transcriptional regulation, and environmental pressures in evolutionary biology. Full article

Transposable elements (TEs) are crucial for genome evolution and ecological adaptation, but their dynamics in non-model plants are poorly understood. Using genomic, transcriptomic, and population genomic approaches, we analyzed the TE landscape of Barthea barthei (Melastomataceae), a species distributed across tropical and subtropical southern China. We identified 64,866 TE copies (16.76% of a 235 Mb genome), dominated by Ty3/Gypsy retrotransposons (8.82%) and DNA/Mutator elements (2.7%). A genome-wide analysis revealed 13 TE islands enriched in genes related to photosynthesis, tryptophan metabolism, and stress response. We identified 3859 high-confidence TE insertion polymorphisms (TIPs), including 29 fixed insertions between red and white flower ecotypes, affecting genes involved in cell wall modification, stress response, and secondary metabolism. A transcriptome analysis of the flower buds identified 343 differentially expressed TEs between the ecotypes, 30 of which were near or within differentially expressed genes. The non-random distribution (primarily within 5 kb of genes) and association with adaptive traits suggest a significant role in B. barthei’s successful colonization of diverse habitats. Our findings provide insights into how TEs contribute to plant genome evolution and ecological adaptation in tropical forests, particularly through their influence on regulatory networks governing stress response and development. Full article

Adaptive changes encompass physiological, morphological, or behavioral modifications occurring in organisms in response to specific environmental conditions. These modifications may become established within a population through natural selection. While adaptive changes can influence individuals or populations over short timeframes, evolution involves the inheritance and accumulation of these changes over extended periods under environmental pressures through natural selection. At present, addressing climate change, emerging infectious diseases, and food security are the main challenges faced by scientists. A comprehensive and profound understanding of the mechanisms of adaptive evolution is of great significance for solving these problems. The genetic basis of these adaptations can be examined through classical genetics, which includes stochastic gene mutations and chromosomal instability, as well as epigenetics, which involves DNA methylation and histone modifications. These mechanisms not only govern the rate and magnitude of adaptive changes but also affect the transmission of adaptive traits to subsequent generations. In the study of adaptive changes under controlled conditions, short-term controlled experiments are commonly utilized in microbial and animal research to investigate long-term evolutionary trends. However, the application of this approach in plant research remains limited. This review systematically compiles the findings on adaptive changes and their genetic foundations in organisms within controlled environments. It aims to provide valuable insights into fundamental evolutionary processes, offering novel theoretical frameworks and research methodologies for future experimental designs, particularly in the field of plant studies. Full article

We introduce BERT mutation, a novel, domain-independent mutation operator for Genetic Programming (GP) that leverages advanced Natural Language Processing (NLP) techniques to improve convergence, particularly using the Masked Language Modeling approach. By combining the capabilities of deep reinforcement learning and the BERT transformer architecture, BERT mutation intelligently suggests node replacements within GP trees to enhance their fitness. Unlike traditional stochastic mutation methods, BERT mutation adapts dynamically by using historical fitness data to optimize mutation decisions, resulting in more effective evolutionary improvements. Through comprehensive evaluations across three benchmark domains, we demonstrate that BERT mutation significantly outperforms conventional and state-of-the-art mutation operators in terms of convergence speed and solution quality. This work represents a pivotal step toward integrating state-of-the-art deep learning into evolutionary algorithms, pushing the boundaries of adaptive optimization in GP. Full article

The prevalence of antimicrobial resistance (AMR) in bacterial pathogens resulting from the intensive usage of antibiotics and antibiotic compounds is acknowledged as a significant global concern that impacts both human and animal health. In this study, we sequenced and analyzed the genomes of two emergent onion-pathogenic species of Burkholderia, B. cenocepacia CCRMBC56 and B. orbicola CCRMBC23, focusing on genes that are potentially associated with their high level of antibiotic and copper resistance. We also identified genes contributing to the copper resistance of B. cenocepacia CCRMBC56 through high-throughput analysis of mutated genes in random transposon mutant populations that were differentially enriched in a copper-containing medium. The results indicated that genes involved in DNA integration, recombination, and cation transport are important for the survival of B. cenocepacia CCRMBC56 in copper-stressed conditions. Furthermore, the fitness effect analysis identified additional genes crucial for copper resistance, which are involved in functions associated with the oxidative stress response, the ABC transporter complex, and the cell outer membrane. In the same analysis, genes related to penicillin binding, the TCA cycle, and FAD binding were found to hinder bacterial adaptation to copper toxicity. This study provides potential targets for reducing the copper resistance of B. cenocepacia and other copper-resistant bacterial pathogens. Full article

In late 2021, Eurasian-lineage highly pathogenic avian influenza (HPAI) A(H5N1) viruses from HA clade 2.3.4.4b were first detected in the United States. These viruses have caused severe morbidity and mortality in poultry and have been detected in numerous wild and domestic animals, including cows and humans. Notably, infected cows transmitted the virus to cats, causing extreme pathogenicity and death. While human-to-human spread of the virus has not been recorded, efficient transmission of the bovine-origin virus has also led to extreme pathogenicity and death in ferret models. Recently, markers in PB2 (E627K) and HA (E186D, Q222H), indicating mammalian adaptation mutations, were detected in an H5N1-infected patient manifesting critical illness in Canada. These, combined with instances of interspecies spread of the virus, have raised global public health concerns. This could highlight the potential for the virus to successfully adapt to mammals, posing a serious risk of a global outbreak. A One Health approach is, thereby, necessary to monitor and control the outbreak. This review aims to analyze the epidemiology, transmission, and ecological impacts of HPAI A(H5N1) clade 2.3.4.4b in the U.S., identify knowledge gaps, and inform strategies for effective outbreak management and mitigation. Full article

Background/Objectives: New anti-tuberculosis compounds are needed to treat patients infected with multi- or extensively drug-resistant Mycobacterium tuberculosis strains. Studies based on spontaneous in vitro mutagenesis can provide insights into the possible modes of action and resistance mechanisms of such new compounds. We evaluated the primary response of M. tuberculosis in vitro to the action of new aroylhydrazones and nitrofuroylamides. Methods: The reference strain H37Rv was cultured on solid media with compounds at increased concentrations relative to MIC. Resistant clones were investigated using whole-genome sequencing and bioinformatics tools to assess the role and potential impact of identified mutations. Results: Some of the mutations are significant (based on in silico analysis), located in essential genes, and therefore of particular interest. Frameshift mutations were observed in (i) Rv2702/ppgK, which is associated with starvation-induced drug tolerance and persistence in mice, and (ii) Rv3696c/glpK, which has been described as a switch on/off mutation associated with drug tolerance. Nonsynonymous substitutions were found in Rv0506/mmpS2, which belongs to the Mmp protein family involved in transport and drug efflux, and in infB, encoding the translation initiation factor IF-2. Conclusions: The primary adaptation of M. tuberculosis to the selective pressure of the tested compounds is complex and multifaceted. It involves multiple unrelated genes and pathways linked to non-specific drug tolerance, efflux systems, or mechanisms counteracting oxidative stress. Full article

The discovery, commercialization, and regular administration of antimicrobial agents have revolutionized the therapeutic paradigm, making it possible to treat previously untreatable and fatal infections. However, the excessive use of antibiotics has led to develop resistance soon after their use in clinical practice, to the point of becoming a global emergency. The mechanisms of bacterial resistance to antibiotics are manifold, including mechanisms of destruction or inactivation, target site modification, or active efflux, and represent the main examples of evolutionary adaptation for the survival of bacterial species. The acquirement of new resistance mechanisms is a consequence of the great genetic plasticity of bacteria, which triggers specific responses that result in mutational adaptation, acquisition of genetic material, or alteration of gene expression, virtually producing resistance to all currently available antibiotics. Understanding resistance processes is critical to the development of new antimicrobial agents to counteract drug-resistant microorganisms. In this review, both the mechanisms of action of antibiotic resistance (AMR) and the antibiotic resistance genes (ARGs) mainly found in clinical and environmental bacteria will be reviewed. Furthermore, the evolutionary background of multidrug-resistant bacteria will be examined, and some promising elements to control or reduce the emergence and spread of AMR will be proposed. Full article

Background: Investigating the way in which individuals are genetically related has been a long-standing application of forensic DNA typing. Whilst capillary electrophoresis (CE)-based STR analysis is likely to provide sufficient data to resolve regularly encountered paternity cases, its power to adequately resolve more distant or complex relationships can be limited. Massively parallel sequencing (MPS) has become a popular alternative method to CE for analysing genetic markers for forensic applications, including kinship analysis. Data workflows used in kinship testing are well-characterised for CE-based methodologies but are much less established for MPS. When incorporating this technology into routine relationship casework, modifications to existing procedures will be required to ensure that the full power of MPS can be utilised whilst maintaining the authenticity of results. Methods: Empirical data generated with MPS for forensically relevant STRs and SNPs and real-world case experience have been used to determine the necessary workflow adaptations. Results: The four considerations highlighted in this work revolve around the distinctive properties of sequence-based data and the need to adapt CE-based data analysis workflows to ensure compatibility with existing kinship software. These considerations can be summarised as the need for a suitable sequence-based allele nomenclature; methods to account for mutational events; appropriate population databases; and procedures for dealing with rare allele frequencies. Additionally, a practical outline of the statistical adjustments required to account for genetic linkage between loci, within the expanded marker sets associated with MPS, has been presented. Conclusions: This article provides a framework for laboratories wishing to implement MPS into routine kinship analysis, with guidance on aspects of the data analysis and statistical interpretation processes. Full article

Rosa rugosa is an excellent aromatic plant species valued for both essential oil extraction and ornamental applications. This study aimed to evaluate its adaptive responses, bioaccumulation capacity, and production quality under cadmium (Cd) stress, providing insights for phytoremediation and sustainable agriculture. A controlled pot experiment was conducted using two cultivars (R. rugosa ‘Zizhi’ and its bud mutation R. rugosa ‘Baizizhi’) subjected to various Cd treatments. Growth parameters and physiological indices, such as antioxidant enzyme activities, chlorophyll content, photosynthesis rates, and floral volatile organic compounds, were systematically analyzed. Cd concentrations ranging from 5 to 50 mg·kg⁻¹ maintained plant growth, but significantly elevated antioxidant activities (SOD + 65.94–300.53%, POD + 37.58–75.06%, CAT + 12.48–12.62%) and chlorophyll content (+20.27–242.79%). In contrast, 400 mg·kg⁻¹ Cd severely inhibited growth, inducing chlorosis and leaf desiccation. Total floral volatiles showed a hormetic response, peaking at 200 mg·kg⁻¹ (+46.08%). Sesquiterpenoids showed greater Cd-responsiveness than monoterpenoids, though core aromatic profiles remained stable. The species exhibited root bioconcentration BAF > 0.1 and limited translocation TF < 1, indicating phytostabilization potential. Despite tolerance up to 400 mg·kg⁻¹, field application is recommended below 50 mg·kg⁻¹—a threshold exceeding China’s soil Cd limits (GB 15618-2018). These findings position it as a dual-purpose crop for ecological restoration and fragrance production in Cd-impacted areas. Full article