Due to the population-based and iterative-based characteristics of evolutionary computation (EC) algorithms, parallel techniques have been widely used to speed up the EC algorithms. However, the ...parallelism usually performs in the population level where multiple populations (or subpopulations) run in parallel or in the individual level where the individuals are distributed to multiple resources. That is, different populations or different individuals can be executed simultaneously to reduce running time. However, the research into generation-level parallelism for EC algorithms has seldom been reported. In this article, we propose a new paradigm of the parallel EC algorithm by making the first attempt to parallelize the algorithm in the generation level. This idea is inspired by the industrial pipeline technique. Specifically, a kind of EC algorithm called local version particle swarm optimization (PSO) is adopted to implement a pipeline-based parallel PSO (PPPSO, i.e., P 3 SO). Due to the generation-level parallelism in P 3 SO, when some particles still perform their evolutionary operations in the current generation, some other particles can simultaneously go to the next generation to carry out the new evolutionary operations, or even go to further next generation(s). The experimental results show that the problem-solving ability of P 3 SO is not affected while the evolutionary speed has been substantially accelerated in a significant fashion. Therefore, generation-level parallelism is possible in EC algorithms and may have significant potential applications in time-consumption optimization problems.
Investigation of the marine-derived fungus Pleosporales sp. CF09-1 cultured in modified PDB medium led to the isolation of six new azaphilone derivatives, pleosporalones B and C (1 and 2) and ...pleosporalones E–H (4–7), and one known analogue (3). The absolute configurations of C-2′ and C-3′ in 3 were assigned by a vibrational circular dichroism method. The C-11 relative configurations for the pair of C-11 epimers (4 and 5) were established by comparing the magnitude of the computed 13C NMR chemical shifts (Δδcalcd) with the experimental 13C NMR values (Δδexp) for the epimers. Antiphytopathogenic and anti-Vibrio activities were evaluated for 1–7. Pleosporalone B (1) exhibited potent antifungal activities against the fungi Alternaria brassicicola and Fusarium oxysporum with the same MIC value of 1.6 μg/mL, which were stronger than the positive control ketoconazole among these compounds. Additionally, pleosporalone C (2) displayed significant activity against the fungus Botryosphaeria dothidea (MIC, 3.1 μg/mL). Compounds 6 and 7 displayed moderate anti-Vibrio activities against Vibrio anguillarum and Vibrio parahemolyticus, with MIC values of 13 and 6.3 μg/mL for 6 and 6.3 and 25 μg/mL for 7, respectively.
Iodide in copper's pathway: A new, efficient, and practical copper‐catalyzed synthesis of Z‐iodoenamides from readily available ketoximes has been developed (see scheme). The reaction was believed to ...proceed through a single‐electron‐transfer pathway. The corresponding Z‐iodoenamides have been applied to the synthesis of substituted oxazoles, dienes, β‐phenoxyl enamides, eneynes, β‐acylenamides, and pyrroles (DCE=1,2‐dichloroethane).
The gut microbiota plays a crucial role in coronary artery disease (CAD) development, but limited attention has been given to the role of the microbiota in preventing this disease. This study aimed ...to identify key biomarkers using metagenomics and untargeted metabolomics and verify their associations with atherosclerosis.
A total of 371 participants, including individuals with various CAD types and CAD-free controls, were enrolled. Subsequently, significant markers were identified in the stool samples through gut metagenomic sequencing and untargeted metabolomics. In vivo and in vitro experiments were performed to investigate the mechanisms underlying the association between these markers and atherosclerosis.
Faecal omics sequencing revealed that individuals with a substantial presence of Faecalibacterium prausnitzii had the lowest incidence of CAD across diverse CAD groups and control subjects. A random forest model confirmed the significant relationship between F. prausnitzii and CAD incidence. Notably, F. prausnitzii emerged as a robust, independent CAD predictor. Furthermore, our findings indicated the potential of the gut microbiota and gut metabolites to predict CAD occurrence and progression, potentially impacting amino acid and vitamin metabolism. F. prausnitzii mitigated inflammation and exhibited an antiatherosclerotic effect on ApoE
mice after gavage. This effect was attributed to reduced intestinal LPS synthesis and reinforced mechanical and mucosal barriers, leading to decreased plasma LPS levels and an antiatherosclerotic outcome.
Sequencing of the samples revealed a previously unknown link between specific gut microbiota and atherosclerosis. Treatment with F. prausnitzii may help prevent CAD by inhibiting atherosclerosis.
Abstract
We describe LncACTdb 2.0 (http://www.bio-bigdata.net/LncACTdb/), an updated and significantly expanded database which provides comprehensive information of competing endogenous RNAs (ceRNAs) ...in different species and diseases. We have updated LncACTdb 2.0 with more data and several new features, including (i) manually curating 2663 experimentally supported ceRNA interactions from >5000 published literatures; (ii) expanding the scope of the database up to 23 species and 213 diseases/phenotypes; (iii) curating more ceRNA types such as circular RNAs and pseudogenes; (iv) identifying and scoring candidate lncRNA-associated ceRNA interactions across 33 cancer types from TCGA data; (v) providing illustration of survival, network and cancer hallmark information for ceRNAs. Furthermore, several flexible online tools including LncACT-Get, LncACT-Function, LncACT-Survival, LncACT-Network and LncACTBrowser have been developed to perform customized analysis, functional analysis, survival analysis, network illustration and genomic visualization. LncACTdb 2.0 also provides newly designed, user-friendly web interfaces to search, browse and download all the data. The BLAST interface is convenient for users to query dataset by inputting custom sequences. The Hot points interface provides users the most studied items by others. LncACTdb 2.0 is a continually updated database and will serve as an important resource to explore ceRNAs in physiological and pathological processes.
Key message
A novel MADS-box member
SiMADS34
is essential for regulating inflorescence architecture and grain yield in
Setaria italica.
MADS-box transcription factors participate in regulating ...various developmental processes in plants. Inflorescence architecture is one of the most important agronomic traits and is closely associated with grain yield in most staple crops. Here, we isolated a panicle development mutant
simads34
from a foxtail millet (
Setaria italica
(L.) P. Beauv.) EMS mutant library. The mutant showed significantly altered inflorescence architecture and decreased grain yield. Investigation of agronomic traits revealed increased panicle width by 16.8%, primary branch length by 10%, and number of primary branches by 30.9%, but reduced panicle length by 25.2%, and grain weight by 25.5% in
simads34
compared with wild-type plants. Genetic analysis of a
simads34
× SSR41 F
2
population indicated that the
simads34
phenotype was controlled by a recessive gene. Map-based cloning and bulked-segregant analysis sequencing demonstrated that a single G-to-A transition in the fifth intron of
SiMADS34
in the mutant led to an alternative splicing event and caused an early termination codon in this causal gene.
SiMADS34
mRNA was expressed in all of the tissues tested, with high expression levels at the heading and panicle development stages. Subcellular localization analysis showed that
simads34
predominantly accumulated in the nucleus. Transcriptome sequencing identified 241 differentially expressed genes related to inflorescence development, cell expansion, cell division, meristem growth and peroxide stress in
simads34
. Notably, an SPL14–MADS34–RCN pathway was validated through both RNA-seq and qPCR tests, indicating the putative molecular mechanisms regulating inflorescence development by
SiMADS34
. Our study identified a novel MADS-box member in foxtail millet and provided a useful genetic resource for inflorescence architecture and grain yield research.
Computational intelligence (CI), including artificial neural network, fuzzy logic, and evolutionary computation (EC), has rapidly developed nowadays. Especially, EC is a kind of algorithm for ...knowledge creation and problem solving, playing a significant role in CI and artificial intelligence (AI). However, traditional EC algorithms have faced great challenge of heavy computational burden and long running time in large-scale (e.g., with many variables) problems. How to efficiently extend EC algorithms to solve complex problems has become one of the most significant research topics in CI and AI communities. To this aim, this paper proposes a matrix-based EC (MEC) framework to extend traditional EC algorithms for efficiently solving large-scale or super large-scale optimization problems. The proposed framework is an entirely new perspective on EC algorithm, from the solution representation to the evolutionary operators. In this framework, the whole population (containing a set of individuals) is defined as a matrix, where a row stands for an individual and a column stands for a dimension (decision variable). This way, the parallel computing functionalities of matrix can be directly and easily carried out on the high performance computing resources to accelerate the computational speed of evolutionary operators. This paper gives two typical examples of MEC algorithms, named matrix-based genetic algorithm and matrix-based particle swarm optimization. Their matrix-based solution representations are presented and the evolutionary operators based on the matrix are described. Moreover, the time complexity is analyzed and the experiments are conducted to show that these MEC algorithms are efficient in reducing the computational time on large scale of decision variables. The MEC is a promising way to extend EC to complex optimization problems in big data environment, leading to a new research direction in CI and AI.
The addition of soy sauce residue (SSR) during soybean paste fermentation usually reduces the flavor quality due to high content of fibers. Steam explosion (SE) pretreatment is an effective way to ...promote the fiber degradation. In this study, SE-pretreated SSR was investigated and exploited during soybean paste fermentation. SE pretreatment increased the numbers of holes and the surface irregularity, resulting in a more pronounced wrinkled surface and looser internal structure than other pretreatments. Over half of cellulose and 10 percentage of hemicellulose were released from the dense structure of SE-pretreated SSR. The addition of 3–10 percentage of the SE-pretreated SSR was more suitable for soybean paste fermentation. The flavor formation of SSR during soybean paste fermentation was enhanced by SE pretreatment. In brief, SE pretreatment of SSR improve the quality of soybean paste.
•The dense structure of soy sauce residue was destroyed by steam explosion (SE).•A clearer wrinkled surface and looser inner structure can be formed by SE.•More cellulose and hemicellulose were exposed by SE pretreatment.•Soybean paste flavor was improved by adding 3–10% SE pretreated soy sauce residue.•SE pretreated soy sauce residue was more suitable for soybean paste fermentation.
Alzheimer’s disease (AD), the most common type of senile dementia, includes the complex pathogenesis of abnormal deposition of amyloid beta-protein (Aβ), phosphorylated tau (p-tau) and neuroimmune ...inflammatory. The neurodegenerative process of AD triggers microglial activation, and the overactivation of microglia produces a large number of neuroimmune inflammatory factors. Microglia dysfunction can lead to disturbances in iron metabolism and enhance iron-induced neuronal degeneration in AD, while elevated iron levels in brain areas affect microglia phenotype and function. In this manuscript, we firstly discuss the role of microglia in AD and then introduce the role of microglia in the immune-inflammatory pathology of AD. Their role in AD iron homeostasis is emphasized. Recent studies on microglia and ferroptosis in AD are also reviewed. It will help readers better understand the role of microglia in iron metabolism in AD, and provides a basis for better regulation of iron metabolism disorders in AD and the discovery of new potential therapeutic targets for AD.
PDF
